Merge remote-tracking branch 'origin/main' into update-bootstrap-ui-l…

…ibrary
ComPlat · Oct 9, 2024 · 2f43f6c · 2f43f6c
2 parents fefed4f + cfe6e7e
commit 2f43f6c
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diff --git a/.tool-versions b/.tool-versions
@@ -1,2 +1,2 @@
-nodejs 18.20.3
+nodejs 18.20.4 18.20.3
 ruby 2.7.8
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,6 +1,31 @@
 # Chemotion_ELN Changelog
 ## Latest
 
+## [v1.10.3]
+> (2024-10-02)
+
+* Bug fixes
+  * wellplate template download  ([#2115](https://github.com/ComPlat/chemotion_ELN/pull/2115))
+  * oidc params issue  ([#2190](https://github.com/ComPlat/chemotion_ELN/pull/2190))
+  * admin restore account - rm obsolete has_profile calls  ([#2181](https://github.com/ComPlat/chemotion_ELN/pull/2181))
+  * returning attachment preview when not annotated  ([#2192](https://github.com/ComPlat/chemotion_ELN/pull/2192))
+  * type error when sample has no collection tag data on saving sample  ([#2158](https://github.com/ComPlat/chemotion_ELN/pull/2158))
+
+  ChemSpectra and NMRIUM
+  * internal ref for cv layout  ([#2104](https://github.com/ComPlat/chemotion_ELN/pull/2104))
+
+  UX/UI
+  * reaction scheme - sample names style  ([#2193](https://github.com/ComPlat/chemotion_ELN/pull/2193))
+
+* Chores
+  * Bump express from 4.19.2 to 4.21.0  ([#2154](https://github.com/ComPlat/chemotion_ELN/pull/2154))
+  * Bump dompurify from 2.4.1 to 2.5.6  ([#2157](https://github.com/ComPlat/chemotion_ELN/pull/2157))
+  * bump converter-client 0.11.0  ([#2171](https://github.com/ComPlat/chemotion_ELN/pull/2171))
+  * Bump puma from 5.6.8 to 5.6.9  ([#2168](https://github.com/ComPlat/chemotion_ELN/pull/2168))
+
+* Ci
+  * set postgres to latest 16 for testing  ([#2191](https://github.com/ComPlat/chemotion_ELN/pull/2191))
+
 ## [v1.10.2]
 > (2024-09-13)
 

diff --git a/VERSION b/VERSION
@@ -1,3 +1,3 @@
-version: v1.10.2
-base_revision: 7e269bb594d29413788f3e5bfa16544981b5d392
-current_revision: 7e269bb594d29413788f3e5bfa16544981b5d392
+version: v1.10.3
+base_revision: dfb34c7ce47fa1c0e62a7bc5772752705b8c6816
+current_revision: dfb34c7ce47fa1c0e62a7bc5772752705b8c6816
diff --git a/app/api/chemotion/attachment_api.rb b/app/api/chemotion/attachment_api.rb
@@ -219,31 +219,19 @@ def remove_duplicated(att)
       desc 'get_annotated_image_of_attachment'
       get ':attachment_id/annotated_image' do
         content_type 'application/octet-stream'
-
         env['api.format'] = :binary
 
-        store = @attachment.attachment.storage.directory
-        file_location = store.join(
-          @attachment.attachment_data['derivatives']['annotation']['annotated_file_location'] || 'not available',
-        )
-
-        uploaded_file = if file_location.present? && File.file?(file_location)
-                          extension_of_annotation = File.extname(@attachment.filename)
-                          extension_of_annotation = '.png' if @attachment.attachment.mime_type == 'image/tiff'
-                          filename_of_annotated_image = @attachment.filename.gsub(
-                            File.extname(@attachment.filename),
-                            "_annotated#{extension_of_annotation}",
-                          )
-                          header['Content-Disposition'] = "attachment; filename=\"#{filename_of_annotated_image}\""
-                          File.open(file_location)
-                        else
-                          header['Content-Disposition'] = "attachment; filename=\"#{@attachment.filename}\""
-                          @attachment.attachment_attacher.file
-                        end
-        data = uploaded_file.read
-        uploaded_file.close
-
-        data
+        annotation = @attachment.annotated_file_location.presence
+        if annotation.present? && File.file?(annotation)
+          header['Content-Disposition'] = "attachment; filename=\"#{@attachment.annotated_filename}\""
+          file = File.open(annotation)
+        else
+          header['Content-Disposition'] = "attachment; filename=\"#{@attachment.filename}\""
+          file = @attachment.attachment_attacher.file
+        end
+        file.read
+      ensure
+        file&.close
       end
 
       desc 'update_annotation_of_attachment'
@@ -314,13 +302,12 @@ def remove_duplicated(att)
             next unless att.annotated?
 
             begin
-              annotated_file_name = "#{File.basename(att.filename, '.*')}_annotated#{File.extname(att.filename)}"
-              zip.put_next_entry annotated_file_name
+              zip.put_next_entry att.annotated_filename
               file = File.open(att.annotated_file_location)
               zip.write file.read
-              file_text += "#{annotated_file_name} #{file.size}\n"
+              file_text += "#{att.annotated_filename} #{file.size}\n"
             ensure
-              file.close
+              file&.close
             end
           end
 

diff --git a/app/models/attachment.rb b/app/models/attachment.rb
@@ -237,7 +237,7 @@ def type_image_tiff?
 
   def annotated?
     # attachment['derivatives'].present? && attachment['derivatives']['annotation'].present?
-    attachment_data&.dig('derivatives', 'annotation', 'annotated_file_location')&.present? || false
+    attachment_data&.dig('derivatives', 'annotation', 'annotated_file_location').present? || false
   end
 
   def annotated_image?
@@ -249,6 +249,7 @@ def type_pdf?
     attachment['mime_type'].to_s == 'application/pdf'
   end
 
+  # @return [String] the path to the combined image file on disk
   def annotated_file_location
     return '' unless annotated?
 
@@ -258,6 +259,15 @@ def annotated_file_location
     )
   end
 
+  # @return [String] build annotation file name based on the original file name
+  def annotated_filename
+    return '' unless annotated?
+
+    # NB: original tiff file are converted to png for the annotation background layer
+    extension_of_annotation = content_type == 'image/tiff' ? '.png' : File.extname(filename)
+    "#{File.basename(filename, '.*')}_annotated#{extension_of_annotation}"
+  end
+
   def preview
     "data:image/png;base64,#{Base64.encode64(read_thumbnail)}" if thumb
   end

diff --git a/app/packs/src/apps/mydb/elements/details/reactions/schemeTab/Material.js b/app/packs/src/apps/mydb/elements/details/reactions/schemeTab/Material.js
@@ -942,11 +942,9 @@ class Material extends Component {
     };
 
     const idCheck = /^\d+$/;
-    const truncatedSampleName = material.molecule_iupac_name?.length > 20 && materialGroup === 'reactants'
-      ? material.molecule_iupac_name?.substring(1, 25) : material.molecule_iupac_name;
 
     if (skipIupacName) {
-      let materialDisplayName = truncatedSampleName || material.name;
+      let materialDisplayName = material.molecule_iupac_name || material.name;
       if (materialGroup === 'solvents' || materialGroup === 'purification_solvents') {
         materialDisplayName = material.external_label || materialDisplayName;
       }
@@ -965,7 +963,7 @@ class Material extends Component {
             tabIndex={0}
             onClick={() => this.handleMaterialClick(material)}
             style={{ cursor: 'pointer' }}
-          ><span className="reaction-material-link">{materialDisplayName}</span></a>
+          ><span>{materialDisplayName}</span></a>
         );
       } else {
         materialName = <span>{materialDisplayName}</span>;
@@ -981,7 +979,7 @@ class Material extends Component {
           tabIndex={0}
           onClick={() => this.handleMaterialClick(material)}
           style={{ cursor: 'pointer' }}
-        ><span className="reaction-material-link">{materialDisplayName}</span></a>
+        ><span>{materialDisplayName}</span></a>
       );
 
       if (material.isNew) { materialName = materialDisplayName; }
@@ -1011,7 +1009,7 @@ class Material extends Component {
             </Button>
           </OverlayTrigger>
           <OverlayTrigger placement="bottom" overlay={iupacNameTooltip(material)}>
-            <div>
+            <div className={'reaction-material-link'}>
               {materialName}
             </div>
           </OverlayTrigger>

diff --git a/prepare-nodejs.sh b/prepare-nodejs.sh
@@ -30,7 +30,7 @@ if [ -z "$nodeversion" ]; then
 fi
 
 # find the latest version of the required version
-REQUIRED_NODE_VERSION=$(asdf list all nodejs | grep -E "$nodeversion" | tail -n1)
+REQUIRED_NODE_VERSION=$(asdf list all nodejs | grep -E "^$nodeversion" | tail -n1)
 
 # Compare the versions
 if [[ "$CURRENT_NODE_VERSION" == "$REQUIRED_NODE_VERSION" ]]; then