feat: add chemspectra with ref peaks

.service-dependencies

@@ -1,5 +1,5 @@
 #syntax=v1
 CONVERTER=ComPlat/[email protected]
 KETCHER=ptrxyz/chemotion-ketchersvc@main
-SPECTRA=ComPlat/chem-spectra-app@0.14.0
+SPECTRA=ComPlat/chem-spectra-app@0.15.0
 NMRIUMWRAPPER=NFDI4Chem/[email protected]

app/api/chemotion/attachment_api.rb

@@ -475,6 +475,7 @@ def remove_duplicated(att)
         optional :cyclicvolta, type: String
         optional :curveIdx, type: Integer
         optional :simulatenmr, type: Boolean
+        optional :axesUnits, type: String
       end
       post 'save_spectrum' do
         jcamp_att = @attachment.generate_spectrum(

app/api/chemotion/chem_spectra_api.rb

@@ -1,6 +1,8 @@
 # frozen_string_literal: true
 
 # Belong to Chemotion module
+
+# rubocop:disable Metrics/ClassLength
 module Chemotion
   # API for ChemSpectra manipulation
   class ChemSpectraAPI < Grape::API
@@ -145,6 +147,60 @@ def raw_file(att)
         post 'refresh' do
           convert_for_refresh(params)
         end
+
+        desc 'Combine spectra'
+        params do
+          requires :spectra_ids, type: [Integer]
+          requires :front_spectra_idx, type: Integer # index of front spectra
+        end
+        post 'combine_spectra' do
+          pm = to_rails_snake_case(params)
+
+          list_file = []
+          list_file_names = []
+          container_id = -1
+          combined_image_filename = ''
+          Attachment.where(id: pm[:spectra_ids]).each do |att|
+            container = att.container
+            combined_image_filename = "#{container.name}.new_combined.png"
+            container_id = att.attachable_id
+            list_file_names.push(att.filename)
+            list_file.push(att.abs_path)
+          end
+
+          _, image = Chemotion::Jcamp::CombineImg.combine(
+            list_file, pm[:front_spectra_idx], list_file_names
+          )
+
+          content_type('application/json')
+          unless image.nil?
+            att = Attachment.find_by(filename: combined_image_filename, attachable_id: container_id)
+            if att.nil?
+              att = Attachment.new(
+                bucket: container_id,
+                filename: combined_image_filename,
+                key: SecureRandom.uuid,
+                created_by: current_user.id,
+                created_for: current_user.id,
+                content_type: 'image/png',
+                file_path: image.path,
+                attachable_type: 'Container',
+                attachable_id: container_id,
+                storage: Rails.configuration.storage.primary_store,
+              )
+              att.save!
+            else
+              att.update!(
+                storage: Rails.configuration.storage.primary_store,
+                file_path: image.path,
+                attachable_type: 'Container',
+                attachable_id: container_id,
+              )
+            end
+          end
+
+          { status: true }
+        end
       end
 
       resource :predict do
@@ -208,3 +264,5 @@ def raw_file(att)
     end
   end
 end
+
+# rubocop:enable Metrics/ClassLength

app/packs/src/apps/mydb/elements/details/ViewSpectra.js

@@ -342,7 +342,8 @@ class ViewSpectra extends React.Component {
 
   writeCommon({
     peaks, shift, scan, thres, analysis, layout, isAscend, decimal, body,
-    keepPred, isIntensity, multiplicity, integration, cyclicvoltaSt, curveSt, waveLength
+    keepPred, isIntensity, multiplicity, integration, cyclicvoltaSt, curveSt,
+    waveLength, axesUnitsSt,
   }, isMpy = false) {
     const { sample, handleSampleChanged } = this.props;
     const si = this.getSpcInfo();
@@ -386,7 +387,7 @@ class ViewSpectra extends React.Component {
 
     const cb = () => (
       this.saveOp({
-        peaks, shift, scan, thres, analysis, keepPred, integration, multiplicity, cyclicvoltaSt, curveSt, waveLength
+        peaks, shift, scan, thres, analysis, keepPred, integration, multiplicity, cyclicvoltaSt, curveSt, waveLength, axesUnitsSt,
       })
     );
     handleSampleChanged(sample, cb);
@@ -403,7 +404,7 @@ class ViewSpectra extends React.Component {
   }
 
   saveOp({
-    peaks, shift, scan, thres, analysis, keepPred, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt, simulatenmr = false
+    peaks, shift, scan, thres, analysis, keepPred, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt, simulatenmr = false, layout, axesUnitsSt,
   }) {
     const { handleSubmit } = this.props;
     const { curveIdx } = curveSt;
@@ -414,14 +415,17 @@ class ViewSpectra extends React.Component {
     const predict = JSON.stringify(rmRefreshed(analysis));
     const waveLengthStr = JSON.stringify(waveLength);
     const cyclicvolta = JSON.stringify(cyclicvoltaSt);
+    const axesUnitsStr = JSON.stringify(axesUnitsSt);
 
     const { shifts } = shift;
     const selectedShift = shifts[curveIdx];
     const { integrations } = integration;
     const selectedIntegration = integrations[curveIdx];
     const { multiplicities } = multiplicity;
     const selectedMutiplicity = multiplicities[curveIdx];
-
+
+    const isSaveCombined = FN.isCyclicVoltaLayout(layout);
+    const { spcInfos } = this.state;
     LoadingActions.start.defer();
     SpectraActions.SaveToFile.defer(
       si,
@@ -438,14 +442,17 @@ class ViewSpectra extends React.Component {
       cyclicvolta,
       curveIdx,
       simulatenmr,
+      spcInfos,
+      isSaveCombined,
+      axesUnitsStr,
     );
   }
 
   refreshOp({
-    peaks, shift, scan, thres, analysis, keepPred, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt
+    peaks, shift, scan, thres, analysis, keepPred, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt, axesUnitsSt,
   }) {
     this.saveOp({
-      peaks, shift, scan, thres, analysis, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt, simulatenmr: true
+      peaks, shift, scan, thres, analysis, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt, simulatenmr: true, axesUnitsSt
     });
   }
 
@@ -471,10 +478,10 @@ class ViewSpectra extends React.Component {
   }
 
   saveCloseOp({
-    peaks, shift, scan, thres, analysis, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt
+    peaks, shift, scan, thres, analysis, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt, layout, axesUnitsSt,
   }) {
     this.saveOp({
-      peaks, shift, scan, thres, analysis, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt
+      peaks, shift, scan, thres, analysis, integration, multiplicity, waveLength, cyclicvoltaSt, curveSt, layout, axesUnitsSt,
     });
     this.closeOp();
   }

app/packs/src/fetchers/AttachmentFetcher.js

@@ -511,7 +511,10 @@ export default class AttachmentFetcher {
     waveLengthStr,
     cyclicvolta,
     curveIdx,
-    simulatenmr
+    simulatenmr,
+    previousSpcInfos,
+    isSaveCombined,
+    axesUnitsStr
   ) {
     const params = {
       attachmentId: attId,
@@ -529,6 +532,7 @@ export default class AttachmentFetcher {
       cyclicvolta: cyclicvolta,
       curveIdx: curveIdx,
       simulatenmr: simulatenmr,
+      axesUnits: axesUnitsStr,
     };
 
     const promise = fetch('/api/v1/attachments/save_spectrum/', {
@@ -541,7 +545,23 @@ export default class AttachmentFetcher {
       body: JSON.stringify(decamelizeKeys(params)),
     })
       .then(response => response.json())
-      .then(json => json)
+      .then((json) => {
+        if (!isSaveCombined) {
+          return json;
+        }
+        const oldSpcInfos = [...previousSpcInfos].filter((spc) => {
+          return spc.idx !== attId;
+        });
+        let jcampIds = oldSpcInfos.map((spc) => (spc.idx));
+        const fetchedFilesIdxs = json.files.map((file) => (file.id));
+        jcampIds = [...jcampIds, ...fetchedFilesIdxs];
+
+        return AttachmentFetcher.combineSpectra(jcampIds, curveIdx).then((res) => {
+          return json;
+        }).catch((errMsg) => {
+          console.log(errMsg); // eslint-disable-line
+        });
+      })
       .catch(errorMessage => {
         console.log(errorMessage);
       });
@@ -640,4 +660,34 @@ export default class AttachmentFetcher {
 
     return promise;
   }
+
+  static combineSpectra(jcampIds, curveIdx) {
+    const promise = fetch(
+      '/api/v1/chemspectra/file/combine_spectra',
+      {
+        credentials: 'same-origin',
+        method: 'POST',
+        headers:
+          {
+            Accept: 'application/json',
+            'Content-Type': 'application/json',
+          },
+        body: JSON.stringify({
+          spectra_ids: jcampIds,
+          front_spectra_idx: curveIdx,
+        }),
+      },
+    )
+      .then((response) => {
+        return response.json();
+      })
+      .then((json) => {
+        return json;
+      })
+      .catch((errorMessage) => {
+        console.log(errorMessage);
+      });
+
+    return promise;
+  }
 }

app/packs/src/stores/alt/actions/SpectraActions.js

@@ -34,9 +34,9 @@ class SpectraActions {
     };
   }
 
-  SaveToFile(spcInfo, peaksStr, shift, scan, thres, integration, multiplicity, predict, cb, keepPred = false, waveLengthStr, cyclicvolta, curveIdx = 0, simulatenmr = false) {
+  SaveToFile(spcInfo, peaksStr, shift, scan, thres, integration, multiplicity, predict, cb, keepPred = false, waveLengthStr, cyclicvolta, curveIdx = 0, simulatenmr = false, previousSpcInfos, isSaveCombined = false, axesUnitsStr) {
     return (dispatch) => {
-      AttachmentFetcher.saveSpectrum(spcInfo.idx, peaksStr, shift, scan, thres, integration, multiplicity, predict, keepPred, waveLengthStr, cyclicvolta, curveIdx, simulatenmr)
+      AttachmentFetcher.saveSpectrum(spcInfo.idx, peaksStr, shift, scan, thres, integration, multiplicity, predict, keepPred, waveLengthStr, cyclicvolta, curveIdx, simulatenmr, previousSpcInfos, isSaveCombined, axesUnitsStr)
         .then((fetchedFiles) => {
           dispatch({ fetchedFiles, spcInfo });
           cb();

lib/chemotion/jcamp.rb

@@ -1,5 +1,7 @@
 # frozen_string_literal: true
 
+# rubocop:disable Metrics/BlockLength
+
 require 'net/http'
 
 # Chemotion module
@@ -114,6 +116,7 @@ def self.build_body(
           cyclic_volta: params[:cyclicvolta],
           jcamp_idx: params[:curve_idx],
           simulatenmr: params[:simulatenmr],
+          axes_units: params[:axes_units],
         }
       end
 
@@ -199,6 +202,43 @@ def self.spectrum_img_gene(path)
         Util.extract_zip(rsp_io)
       end
     end
+
+    # Combine multiple jcamps in one image
+    module CombineImg
+      include HTTParty
+
+      def self.stub_request(files, curve_idx, list_file_names)
+        response = nil
+        url = Rails.configuration.spectra.chemspectra.url
+        api_endpoint = "#{url}/combine_images"
+
+        files_to_read = files.map { |fname| File.open(fname) }
+        begin
+          response = HTTParty.post(
+            api_endpoint,
+            body: {
+              multipart: true,
+              files: files_to_read,
+              jcamp_idx: curve_idx,
+              list_file_names: list_file_names,
+            },
+          )
+        ensure
+          files_to_read.each(&:close)
+        end
+        response
+      end
+
+      def self.combine(files, curve_idx, list_file_names)
+        rsp = stub_request(files, curve_idx, list_file_names)
+        if rsp.code == 200
+          rsp_io = StringIO.new(rsp.body.to_s)
+          Util.extract_zip(rsp_io)
+        else # rubocop:disable Style/EmptyElse
+          nil
+        end
+      end
+    end
   end
 end
 
@@ -403,3 +443,5 @@ def self.jcamp_from_nmrium(path)
     end
   end
 end
+
+# rubocop:enable Metrics/BlockLength

package.json

@@ -11,7 +11,7 @@
     "@babel/preset-react": "7.10.4",
     "@citation-js/plugin-isbn": "0.3.0",
     "@complat/chem-spectra-client": "1.0.0-rc20.patch-1",
-    "@complat/react-spectra-editor": "1.0.0-rc20.patch-1",
+    "@complat/react-spectra-editor": "1.0.0-beta.1",
     "@material-ui/core": "^4.12.4",
     "@material-ui/icons": "^4.11.3",
     "@novnc/novnc": "^1.2.0",