780 enhencing versioning feature #800

Allenskywalker92 · 2022-07-15T07:52:09Z

Allenskywalker92 · 2022-07-15T10:56:08Z

mschneider85 · 2022-08-12T07:12:48Z

@Allenskywalker92 I had a notification/mention about this PR that I can no longer find. Has the problem been resolved in the meantime?

Allenskywalker92 · 2022-08-12T07:16:52Z

@mschneider85 I don't know either. Couldn't find any comment.

adambasha0 · 2022-08-19T08:38:29Z

Revert function in the histroy tab of reactions does not work. Also name field in history is empty if the sample has no name. I think maybe it would be better to have common name of any other type of sample identification, so that user can have an idea which sample is this? - or what do you think?

revert_function_doesNotWork.mp4

* removed .match from integer parameter * add fixture for spectrum params * fixed parameter json * add test for edit a jcamp file - WIP * Switch state to done after creating all sub attachments and deleting all files Co-authored-by: FabianMauz <[email protected]>

* - upgrade html2pdf.js to version 0.10.1 - add process as dev dependency to solve webpack compilation error * move process/browser modules to webpack custom file Co-authored-by: Mehreen <mehreen.mansur>

Bumps [decode-uri-component](https://github.com/SamVerschueren/decode-uri-component) from 0.2.0 to 0.2.2. - [Release notes](https://github.com/SamVerschueren/decode-uri-component/releases) - [Commits](SamVerschueren/decode-uri-component@v0.2.0...v0.2.2) --- updated-dependencies: - dependency-name: decode-uri-component dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Current link to docs (https://www.chemotion.net/chemotionsaurus/docs/category/manual) is broken, returns 500.

* obey rubocop rules and removed unused methods * removed no more used methods: store_tmp_file_and_thumbnail, store_file_and_thumbnail_for_dup, move_from_store * Moved attachment logic to after save callback * add tests for attachment model * removed duplicate test * refactor attachment_api * moved attach actions to after save hook * Moved attachment logic to after save callback - report template api * removed validation before save * nothing was validated * Extract creation of report_template to usecase * add size validation of attached file * only attach file if path to file exists * Moved attachment logic to after save callback - generic helpers * tests must be updated * add validation of file size * refactor tests for generic_helpers * more refactoring needed, but first i have to understand the method signatures * Moved attachment logic to after save callback - jcamp_aasm * update to latest dev5 * Moved attachment logic to after save callback - upload_chunk_complete * Moved attachment logic to after save callback - report_templates.seed.db * update to latest dev5 * Move attachment logic to after save callback - sample usecase * update to latest dev5 * Moved attachment logic to after save callback - SampleTask::Update * Moved attachment logic to after save callback - coverter.rb * add file_path to attachment * Fixed bugs and added test * Moved attachment logic to after save callback - datacollector_file.rb * Moved attachment logic to after save callback - datacollector_file.rb - sftp * Moved attachment logic to after save callback - datacollector_folder.rb * removed manual file attaching in test * repaired factory for reports * renamed test folder as in src package * Moved attachment logic to after save callback - datacollector/mailcollector.rb * Moved attachment logic to after save callback - import/import_collections.rb * Moved attachment logic to after save callback - Reporter/worker.rb * add test for creating attachment in worker * Update to latest main * removed useless test * set fixed key to test attachment * fixed bug in test * fixed bug in test (2) * fixed location of files in test * reintroduce test for checking attaching files * update to current main * linted attachment_api.rb * linted generic_helpers.rb * linted attachment.rb * linted upload_chunk_complete.rb * linted import_collections.rb * linted sample_api_spec.rb * linted generic_helpers_spec.rb * add linting for factories: attachments, reports * linted import_wellplate_spreadsheet_spec.rb * removed customized local development folder * add a linebreak to see why rubocop is annoyed * add a linebreak to see why rubocop is annoyed * update to latest main * removed override of key attribute, which leads to further errors * if the key from the frontend is overritten, further updating of container hierarchy will fail * remove duplicate line Co-authored-by: Jan C. Brammer <[email protected]> Co-authored-by: Fabian <fabian@fabian-Virtual-Machine> Co-authored-by: FabianMauz <[email protected]>

* Add SampleTask Inbox (unfinished) * Extract FreeScanCard to allow for individual Sample Dropzones per Task * Add a drop receptacle to open free scans * Update admin app to use newer react-dnd syntax * Fix component reuse bug * Add SampleTask creation dropzone * Fix crashing drag and drop functionality in table sorting popovers Newer versions of react-dnd use React-Contexts to access their DragAndDropManager instance. This instance is wrapped around the toplevel App object in packs/src/apps/{mydb,admin}/index.js Unfortunately, the ancient react-bootstrap package appends Overlays created by an OverlayTrigger OUTSIDE the react tree, so any component that relies on the react tree to supply contexts can no longer access them when inside an overlay. To rectify this, all instances where a drag and drop enabled component is used within an overlay have been rewritten not to use OverlayTrigger. The implemented solution was inspired by the example at https://react-bootstrap-v3.netlify.app/components/overlays/#custom-overlays-overlay * Fix missing Hide box for element list settings * Fix DND integration in Admin App * Move all SampleTaskInbox related files into the same folder

Bumps [loofah](https://github.com/flavorjones/loofah) from 2.19.0 to 2.19.1. - [Release notes](https://github.com/flavorjones/loofah/releases) - [Changelog](https://github.com/flavorjones/loofah/blob/main/CHANGELOG.md) - [Commits](flavorjones/loofah@v2.19.0...v2.19.1) --- updated-dependencies: - dependency-name: loofah dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [rails-html-sanitizer](https://github.com/rails/rails-html-sanitizer) from 1.4.3 to 1.4.4. - [Release notes](https://github.com/rails/rails-html-sanitizer/releases) - [Changelog](https://github.com/rails/rails-html-sanitizer/blob/master/CHANGELOG.md) - [Commits](rails/rails-html-sanitizer@v1.4.3...v1.4.4) --- updated-dependencies: - dependency-name: rails-html-sanitizer dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [nokogiri](https://github.com/sparklemotion/nokogiri) from 1.13.9 to 1.13.10. - [Release notes](https://github.com/sparklemotion/nokogiri/releases) - [Changelog](https://github.com/sparklemotion/nokogiri/blob/main/CHANGELOG.md) - [Commits](sparklemotion/nokogiri@v1.13.9...v1.13.10) --- updated-dependencies: - dependency-name: nokogiri dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [httparty](https://github.com/jnunemaker/httparty) from 0.20.0 to 0.21.0. - [Release notes](https://github.com/jnunemaker/httparty/releases) - [Changelog](https://github.com/jnunemaker/httparty/blob/master/Changelog.md) - [Commits](jnunemaker/httparty@v0.20.0...v0.21.0) --- updated-dependencies: - dependency-name: httparty dependency-type: direct:production ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [json5](https://github.com/json5/json5) from 1.0.1 to 1.0.2. - [Release notes](https://github.com/json5/json5/releases) - [Changelog](https://github.com/json5/json5/blob/main/CHANGELOG.md) - [Commits](json5/json5@v1.0.1...v1.0.2) --- updated-dependencies: - dependency-name: json5 dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* WIP add react flow display * Add first version of editor * Add component_graph_data field to screen model * Update Screen API to allow saving component graph data * Fix typo preventing proper code highlighting * Add component graph data to JS Screen model * Enable saving/updating of component graph data to server and fix static preview display * Make API work properly with specs and update specs to test saving process * Rubocop * Allow relabeling edges in ResearchplanFlowEditor * Assign default width to flow panel * Fix display update issues * Allow dragging and zooming in the component graph preview * Add number of analyses and attachments to EmbeddedResearchPlan within Screen Co-authored-by: Johannes Haubold <[email protected]>

* Improve Dev setup for M1 macs M1 macs use an ARM-based processor architecture, which will be picked up by docker generating ARM linux images by default. So we specifically use the linux/amd64 image to create a non-ARM image to work with. This way all compilation and package installations (google-chrome-stable does not have ARM packages for example) run the expected way. Another issue is that docker for mac uses qemu as backend on M1 macs, which does not support inotify. Because of that, the EventedFileWatcher used in the development environment does not work and had to be replaced by a FileWatcher without usage of inotify * Add database setup to run-ruby-dev.sh

…1091)

* add new values to reagents list * add new values to solvents list * add new purification method in Scheme tab of reaction * refactor the code to fix linting issues Refs: #1433 #562

* fix: fixed reaction to response from the literatures api * style: apply eslint / rubocop rules * refactor: use UrlSearchParams instead of string concat * refactor: extract request params * feat: add ui response after removing literal * style: line length and correct isNaN usage * style: use deconstruction * test: add test for deleting literature * refactor: refactored and styled tests Refs: #1502

* chore: update node LTS to 18 * ci image with upg node version * test(js): force mocha to exit * chore(js): upg whatwg fetch 2->3 * chore(js): upg test dependencies: jsdom, mocha, sinon * devcontainer --------- Co-authored-by: Jan C. Brammer <[email protected]> Refs: #1489

* build(deps): bump citation-js to 0.6.8 * build: remove library patch in post_install script * feat: patch citation-js library to accept also SICIs Refs: #1486

Refs: #1506

Co-authored-by: Lan Le <[email protected]> Refs: #1507

fix: cannot read processed data from Bruker Co-authored-by: Lan Le <[email protected]> Refs: #1528

* Add (de)select all for datasets in device box * select all attachments in a dataset * separate unsortedbox and devicebox checkedIds * correct deleteCheckedDataset function * reset checkedDeviceIds when changing pages * move checkedDeviceIds to InboxStore * handle dataset attachments selection in inboxstore * update handlePrev / NextClick fix: pagination fix: deleteCheckedDataset to delete attachments Refs: #1437

… disable error message for decoupled samples Refs: #1531

github-actions · 2023-09-18T11:09:38Z

app/api/chemotion/admin_generic_api.rb

+          template = { uuid: uuid, layers: {}, select_options: {} }
+          attributes = declared(params, include_missing: false)
+          attributes[:properties_template]['uuid'] = uuid if attributes[:properties_template].present?
+          attributes[:properties_template] = template unless attributes[:properties_template].present?


Rails/Blank: Use if attributes[:properties_template].blank? instead of unless attributes[:properties_template].present?.

github-actions · 2023-09-18T11:09:39Z

app/api/chemotion/admin_generic_api.rb

+          attributes = declared(params, include_missing: false)
+          attributes[:properties_template]['uuid'] = uuid if attributes[:properties_template].present?
+          attributes[:properties_template] = template unless attributes[:properties_template].present?
+          attributes[:properties_template]['eln'] = Chemotion::Application.config.version if attributes[:properties_template].present?


Style/IfUnlessModifier: Modifier form of if makes the line too long.

github-actions · 2023-09-18T11:09:39Z

app/api/chemotion/admin_generic_api.rb

+          attributes = declared(params, include_missing: false)
+          attributes[:properties_template]['uuid'] = uuid if attributes[:properties_template].present?
+          attributes[:properties_template] = template unless attributes[:properties_template].present?
+          attributes[:properties_template]['eln'] = Chemotion::Application.config.version if attributes[:properties_template].present?


Layout/LineLength: Line is too long. [134/120]

github-actions · 2023-09-18T11:09:39Z

app/api/chemotion/admin_generic_api.rb

+          klasses = ElementKlass.where(is_active: true)&.pluck(:name) || []
+          bytes_written = File.write(klass_names_file, klasses)
+          if bytes_written == klasses.length
+            puts "File successfully written"


Rails/Output: Do not write to stdout. Use Rails's logger if you want to log.

github-actions · 2023-09-18T11:09:39Z

app/api/chemotion/admin_generic_api.rb

+          klasses = ElementKlass.where(is_active: true)&.pluck(:name) || []
+          bytes_written = File.write(klass_names_file, klasses)
+          if bytes_written == klasses.length
+            puts "File successfully written"


Style/StringLiterals: Prefer single-quoted strings when you don't need string interpolation or special symbols.

github-actions · 2023-09-18T11:09:40Z

app/api/chemotion/chemical_api.rb

+        params do
+          requires :sample_id, type: Integer, desc: 'sample id'
+          requires :cas, type: String
+          requires :chemical_data, type: Array[Hash]


Style/RedundantArrayConstructor: Remove the redundant Array constructor.

github-actions · 2023-09-18T11:09:40Z

app/api/chemotion/collection_api.rb

@@ -19,6 +21,42 @@ class CollectionAPI < Grape::API
        get do
          present Collection.find(params[:id]), with: Entities::CollectionEntity, root: :collection
        end
+
+        desc "Return collection metadata"


Style/StringLiterals: Prefer single-quoted strings when you don't need string interpolation or special symbols.

github-actions · 2023-09-18T11:09:40Z

app/api/chemotion/collection_api.rb

+          error!('401 Unauthorized', 401)
+        end
+        before do
+          error!('401 Unauthorized', 401) unless CollectionPolicy.new(current_user, Collection.find(params[:id])).read_metadata?


Style/IfUnlessModifier: Modifier form of unless makes the line too long.

github-actions · 2023-09-18T11:09:41Z

app/api/chemotion/collection_api.rb

+          error!('401 Unauthorized', 401)
+        end
+        before do
+          error!('401 Unauthorized', 401) unless CollectionPolicy.new(current_user, Collection.find(params[:id])).read_metadata?


Layout/LineLength: Line is too long. [128/120]

github-actions · 2023-09-18T11:09:41Z

app/api/chemotion/collection_api.rb

+        end
+        get :metadata do
+          metadata = Metadata.where(collection_id: params[:id]).first
+          if metadata


Style/RedundantCondition: Use double pipes || instead.

github-actions · 2023-09-18T11:09:45Z

app/api/chemotion/collection_api.rb

+          end
+        end
+
+        desc "Create/update collection metadata"


Style/StringLiterals: Prefer single-quoted strings when you don't need string interpolation or special symbols.

github-actions · 2023-09-18T11:09:45Z

app/api/chemotion/collection_api.rb

+          requires :metadata, type: JSON
+        end
+        before do
+          error!('401 Unauthorized', 401) unless CollectionPolicy.new(current_user, Collection.find(params[:id])).update_metadata?


Style/IfUnlessModifier: Modifier form of unless makes the line too long.

github-actions · 2023-09-18T11:09:45Z

app/api/chemotion/collection_api.rb

+          requires :metadata, type: JSON
+        end
+        before do
+          error!('401 Unauthorized', 401) unless CollectionPolicy.new(current_user, Collection.find(params[:id])).update_metadata?


Layout/LineLength: Line is too long. [130/120]

github-actions · 2023-09-18T11:09:45Z

app/api/chemotion/collection_api.rb

+        end
+        post :metadata do
+          metadata = Metadata.where(collection_id: params[:id]).first
+          unless metadata


Style/IfUnlessModifier: Favor modifier unless usage when having a single-line body. Another good alternative is the usage of control flow &&/||.

github-actions · 2023-09-18T11:09:45Z

app/api/chemotion/collection_api.rb

+        end
+        post :metadata do
+          metadata = Metadata.where(collection_id: params[:id]).first
+          unless metadata


Style/OrAssignment: Use the double pipe equals operator ||= instead.

github-actions · 2023-09-18T11:09:47Z

app/api/chemotion/search_api.rb

@@ -331,24 +340,23 @@ def search_elements(c_id = @c_id, dl = @dl)
                end

        if search_method == 'advanced' && molecule_sort == false
-          arg_value_str = adv_params.first['value'].split(/(\r)?\n|,/).map(&:strip)
+          arg_value_str = adv_params.first['value'].split(/(\r)?\n/).map(&:strip)


Style/InverseMethods: Use reject instead of inverting select.

github-actions · 2023-09-18T11:09:47Z

app/api/chemotion/search_api.rb

@@ -470,6 +478,8 @@ def elements_by_scope(scope, collection_id = @c_id)
            case search_by_method
            when 'structure'
              sample_structure_search
+            when 'cas'
+              Sample.by_collection_id(@c_id).by_sample_xref_cas( params[:selection][:name])


Layout/SpaceInsideParens: Space inside parentheses detected.

github-actions · 2023-09-18T11:09:47Z

app/api/chemotion/suggestion_api.rb

@@ -63,9 +63,11 @@ def search_possibilities_by_type_user_and_collection(type)
          sample_name = dl_s.positive? && search_by_field.call(Sample, :name, qry) || []
          polymer_type = dl_s.positive? && d_for.call(Sample)
                                                .by_residues_custom_info('polymer_type', qry)
-                                                .pluck("residues.custom_info -> 'polymer_type'").uniq || []
+                                                .pluck(Arel.sql("residues.custom_info->'polymer_type'")).uniq || []


Metrics/AbcSize: Assignment Branch Condition size for search_possibilities_by_type_user_and_collection is too high. [<66, 148, 116> 199.3/25]

github-actions · 2023-09-18T11:09:47Z

app/api/chemotion/suggestion_api.rb

@@ -63,9 +63,11 @@ def search_possibilities_by_type_user_and_collection(type)
          sample_name = dl_s.positive? && search_by_field.call(Sample, :name, qry) || []
          polymer_type = dl_s.positive? && d_for.call(Sample)
                                                .by_residues_custom_info('polymer_type', qry)
-                                                .pluck("residues.custom_info -> 'polymer_type'").uniq || []
+                                                .pluck(Arel.sql("residues.custom_info->'polymer_type'")).uniq || []


Metrics/CyclomaticComplexity: Cyclomatic complexity for search_possibilities_by_type_user_and_collection is too high. [98/7]

github-actions · 2023-09-18T11:09:47Z

app/api/chemotion/suggestion_api.rb

@@ -63,9 +63,11 @@ def search_possibilities_by_type_user_and_collection(type)
          sample_name = dl_s.positive? && search_by_field.call(Sample, :name, qry) || []
          polymer_type = dl_s.positive? && d_for.call(Sample)
                                                .by_residues_custom_info('polymer_type', qry)
-                                                .pluck("residues.custom_info -> 'polymer_type'").uniq || []
+                                                .pluck(Arel.sql("residues.custom_info->'polymer_type'")).uniq || []


Metrics/MethodLength: Method has too many lines. [135/30]

github-actions · 2023-09-18T11:12:56Z

app/api/chemotion/suggestion_api.rb

@@ -63,9 +63,11 @@ def search_possibilities_by_type_user_and_collection(type)
          sample_name = dl_s.positive? && search_by_field.call(Sample, :name, qry) || []
          polymer_type = dl_s.positive? && d_for.call(Sample)
                                                .by_residues_custom_info('polymer_type', qry)
-                                                .pluck("residues.custom_info -> 'polymer_type'").uniq || []
+                                                .pluck(Arel.sql("residues.custom_info->'polymer_type'")).uniq || []


Metrics/PerceivedComplexity: Perceived complexity for search_possibilities_by_type_user_and_collection is too high. [97/8]

github-actions · 2023-09-18T11:12:56Z

app/api/chemotion/suggestion_api.rb

@@ -63,9 +63,11 @@ def search_possibilities_by_type_user_and_collection(type)
          sample_name = dl_s.positive? && search_by_field.call(Sample, :name, qry) || []
          polymer_type = dl_s.positive? && d_for.call(Sample)
                                                .by_residues_custom_info('polymer_type', qry)
-                                                .pluck("residues.custom_info -> 'polymer_type'").uniq || []
+                                                .pluck(Arel.sql("residues.custom_info->'polymer_type'")).uniq || []


Lint/AmbiguousOperatorPrecedence: Wrap expressions with varying precedence with parentheses to avoid ambiguity.

github-actions · 2023-09-18T11:12:56Z

app/api/chemotion/suggestion_api.rb

          sum_formula = dl_s.positive? && search_by_field.call(Sample, :molecule_sum_formular, qry) || []
          iupac_name = dl_s.positive? && search_by_field.call(Molecule, :iupac_name, qry) || []
+          # cas = dl_s.positive? && search_by_field.call(Molecule, :cas, qry) || []
+          cas = dl_s.positive? && search_by_field.call(Sample, :sample_xref_cas, qry) || []


Lint/AmbiguousOperatorPrecedence: Wrap expressions with varying precedence with parentheses to avoid ambiguity.

github-actions · 2023-09-18T11:12:56Z

app/api/chemotion/suggestion_api.rb

@@ -128,9 +131,11 @@ def search_possibilities_by_type_user_and_collection(type)
          sample_external_label = dl_s > -1 && search_by_field.call(Sample, :external_label, qry) || []
          polymer_type = dl_s.positive? && d_for.call(Sample)
                                                .by_residues_custom_info('polymer_type', qry)
-                                                .pluck("residues.custom_info -> 'polymer_type'").uniq || []
+                                                .pluck(Arel.sql("residues.custom_info->'polymer_type'")).uniq || []


Lint/AmbiguousOperatorPrecedence: Wrap expressions with varying precedence with parentheses to avoid ambiguity.

github-actions · 2023-09-18T11:12:56Z

app/api/chemotion/suggestion_api.rb

          sum_formula = dl_s.positive? && search_by_field.call(Sample, :molecule_sum_formular, qry) || []
          iupac_name = dl_s.positive? && search_by_field.call(Molecule, :iupac_name, qry) || []
+          # cas = dl_s.positive? && search_by_field.call(Molecule, :cas, qry) || []
+          cas = dl_s.positive? && search_by_field.call(Sample, :sample_xref_cas, qry) || []


Lint/AmbiguousOperatorPrecedence: Wrap expressions with varying precedence with parentheses to avoid ambiguity.

github-actions · 2023-09-18T11:12:58Z

app/api/helpers/container_helpers.rb

@@ -79,7 +79,7 @@ def create_or_update_attachments(container, attachments)
    return unless can_update
    attachments.each do |att|
      if att[:is_new]
-        attachment = Attachment.where(storage: 'tmp', key: att[:id]).last
+        attachment = Attachment.where(key: att[:id], attachable: nil).last


Metrics/PerceivedComplexity: Perceived complexity for create_or_update_attachments is too high. [11/8]

github-actions · 2023-09-18T11:12:58Z

app/api/helpers/generic_helpers.rb


+      ensure


Layout/EmptyLinesAroundExceptionHandlingKeywords: Extra empty line detected before the ensure.

github-actions · 2023-09-18T11:12:58Z

app/api/helpers/report_helpers.rb

@@ -460,6 +460,7 @@ def build_sql_reaction_sample(columns, c_id, ids, checkedAll = false)
      sample: {
        external_label: ['s.external_label', '"sample external label"', 0],
        name: ['s."name"', '"sample name"', 0],
+        cas: ['s.xref', nil, 0],


Metrics/ModuleLength: Module has too many lines. [545/100]

github-actions · 2023-09-18T11:12:59Z

app/api/helpers/report_helpers.rb

@@ -570,6 +571,8 @@ def build_column_query(sel, user_id = 0, attrs = EXP_MAP_ATTR)
          selection << "labels_by_user_sample(#{user_id}, s_id) as user_labels"
        elsif col == 'literature'
          selection << "literatures_by_element('Sample', s_id) as literatures"
+        elsif col == 'cas'


Metrics/CyclomaticComplexity: Cyclomatic complexity for build_column_query is too high. [9/7]

github-actions · 2023-09-18T11:12:59Z

app/api/helpers/report_helpers.rb

@@ -570,6 +571,8 @@ def build_column_query(sel, user_id = 0, attrs = EXP_MAP_ATTR)
          selection << "labels_by_user_sample(#{user_id}, s_id) as user_labels"
        elsif col == 'literature'
          selection << "literatures_by_element('Sample', s_id) as literatures"
+        elsif col == 'cas'


Metrics/PerceivedComplexity: Perceived complexity for build_column_query is too high. [10/8]

github-actions · 2023-09-18T11:13:02Z

app/api/modules/logidze_module.rb

+      Logidze.clear_responsible! if @logidze_meta_set.present?
+    end
+  end
+end


Layout/TrailingEmptyLines: Final newline missing.

github-actions · 2023-09-18T11:13:02Z

app/controllers/application_controller.rb

@@ -11,7 +11,7 @@ class ApplicationController < ActionController::Base

  def configure_permitted_parameters
    devise_parameter_sanitizer.permit(:sign_up, keys: [
-      :email, :first_name, :last_name, :name_abbreviation, :omniauth_provider, :omniauth_uid,
+      :email, :first_name, :last_name, :name_abbreviation, :provider, :uid,


Layout/FirstArrayElementIndentation: Use 2 spaces for indentation in an array, relative to the first position after the preceding left parenthesis.

github-actions · 2023-09-18T11:13:02Z

app/controllers/oauth/radar_controller.rb

@@ -0,0 +1,111 @@
+class Oauth::RadarController < ApplicationController


Style/FrozenStringLiteralComment: Missing frozen string literal comment.

github-actions · 2023-09-18T11:13:02Z

app/controllers/oauth/radar_controller.rb

@@ -0,0 +1,111 @@
+class Oauth::RadarController < ApplicationController


Style/ClassAndModuleChildren: Use nested module/class definitions instead of compact style.

github-actions · 2023-09-18T11:13:02Z

app/controllers/oauth/radar_controller.rb

+    collection_id = request.GET['collection_id']
+    unless collection_id
+      @error = 'No collection id was provided.'
+      return render status: 400


Rails/HttpStatus: Prefer :bad_request over 400 to define HTTP status code.

github-actions · 2023-09-18T11:13:06Z

app/controllers/oauth/radar_controller.rb

+      @workspaces = response['data'].map { |workspace| {
+        'id' => workspace['id'],
+        'label' => workspace['descriptiveMetadata']['title']
+      }}


Layout/BlockEndNewline: Expression at 80, 8 should be on its own line.

github-actions · 2023-09-18T11:13:06Z

app/controllers/oauth/radar_controller.rb

+
+      # check if any workspaces were found
+      if @workspaces.empty?
+        @error = 'No workspaces could be retrieved from RADAR. Please make sure that at least one workspace is available.'


Layout/LineLength: Line is too long. [122/120]

github-actions · 2023-09-18T11:13:06Z

app/controllers/oauth/radar_controller.rb

+      # check if any workspaces were found
+      if @workspaces.empty?
+        @error = 'No workspaces could be retrieved from RADAR. Please make sure that at least one workspace is available.'
+        return render status: 400


Rails/HttpStatus: Prefer :bad_request over 400 to define HTTP status code.

github-actions · 2023-09-18T11:13:06Z

app/controllers/oauth/radar_controller.rb

+    collection = Collection.belongs_to_or_shared_by(current_user.id, current_user.group_ids).find_by(id: collection_id)
+    unless collection
+      @error = 'You are not allowed to access this collection.'
+      return render status: 403


Rails/HttpStatus: Prefer :forbidden over 403 to define HTTP status code.

github-actions · 2023-09-18T11:13:06Z

app/controllers/oauth/radar_controller.rb

+      return render status: 403
+    end
+
+    unless collection.metadata.metadata['datasetUrl'].nil?


Style/GuardClause: Use a guard clause (return redirect_to collection.metadata.metadata['datasetUrl'] unless collection.metadata.metadata['datasetUrl'].nil?) instead of wrapping the code inside a conditional expression.

This commit refactors `ReactionDetails` and `SampleDetails` to make them pass eslint checks. We had unused functions there, which will be removed by this commit: - SampleDetails#initiateAnalysisButton - SampleDetails#initiateAnalysisWithKind - SampleDetails#transferToDeviceButton Also disables `forbid-prop-types` in .eslintrc for now. This can be taken out later, when we can better specify the propTypes across the entire project.

Store a history which keeps track of every change made to certain entities and add a "History" tab to the Reaction/Sample detail pages. Related entities are displayed in the version history. E.g. Reaction -> ReactionsSample Save timestamp and author of the version with the changes. A change diff to the previous version can be displayed. Tracked entities: - Attachment - Container - ElementalComposition - Reaction - ReactionsSample - Residue - Sample Co-authored-by: VadimKeller <[email protected]>

This commit refactors `ReactionDetails` and `SampleDetails` to make them pass eslint checks. We had unused functions there, which will be removed by this commit: - SampleDetails#initiateAnalysisButton - SampleDetails#initiateAnalysisWithKind - SampleDetails#transferToDeviceButton Also disables `forbid-prop-types` in .eslintrc for now. This can be taken out later, when we can better specify the propTypes across the entire project.

Store a history which keeps track of every change made to certain entities and add a "History" tab to the Reaction/Sample detail pages. Related entities are displayed in the version history. E.g. Reaction -> ReactionsSample Save timestamp and author of the version with the changes. A change diff to the previous version can be displayed. Tracked entities: - Attachment - Container - ElementalComposition - Reaction - ReactionsSample - Residue - Sample Co-authored-by: VadimKeller <[email protected]>

Add revert button to versioned field reset colum information re-create schema update solvent label

- Update version list after reverting a change - Fix issue /w big svgs - Make reverting molfile / svg work - Fix merge issues - Replace passing local variables /w using state

github-actions · 2023-09-18T11:31:41Z

app/controllers/oauth/radar_controller.rb

+      return render status: 403
+    end
+
+    unless collection.metadata.metadata['datasetUrl'].nil?


Style/UnlessElse: Do not use unless with else. Rewrite these with the positive case first.

github-actions · 2023-09-18T11:31:42Z

app/controllers/oauth/radar_controller.rb

+    end
+
+    unless collection.metadata.metadata['datasetUrl'].nil?
+      return redirect_to collection.metadata.metadata['datasetUrl']


Style/RedundantReturn: Redundant return detected.

github-actions · 2023-09-18T11:31:42Z

app/controllers/oauth/radar_controller.rb

+    unless collection.metadata.metadata['datasetUrl'].nil?
+      return redirect_to collection.metadata.metadata['datasetUrl']
+    else
+      return render


Style/RedundantReturn: Redundant return detected.

github-actions · 2023-09-18T11:31:42Z

app/controllers/users/omniauth_controller.rb

+
+    def first_name
+      if auth&.provider == PROVIDER_GITHUB
+        auth&.info&.name.split[0..-2].join(' ')


Lint/SafeNavigationChain: Do not chain ordinary method call after safe navigation operator.

github-actions · 2023-09-18T11:31:42Z

app/jobs/export_collection_to_radar_job.rb

@@ -0,0 +1,29 @@
+class ExportCollectionToRadarJob < ActiveJob::Base


Style/FrozenStringLiteralComment: Missing frozen string literal comment.

github-actions · 2023-09-18T11:31:44Z

app/models/concerns/attachment_jcamp_aasm.rb

@@ -206,18 +241,22 @@ def update_prediction(params, spc_type, is_regen)
  def create_process(is_regen)
    params = build_params

-    tmp_jcamp, tmp_img, arr_jcamp, arr_img, arr_csv, spc_type = generate_spectrum_data(params, is_regen)
+    if params[:ext] == 'nmrium'


Style/IfUnlessModifier: Favor modifier if usage when having a single-line body. Another good alternative is the usage of control flow &&/||.

github-actions · 2023-09-18T11:31:44Z

app/models/concerns/attachment_jcamp_aasm.rb

+      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)


Lint/UselessAssignment: Useless assignment to variable - arr_nmrium. Use _ or _arr_nmrium as a variable name to indicate that it won't be used.

github-actions · 2023-09-18T11:31:44Z

app/models/concerns/attachment_jcamp_aasm.rb

+      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)


Layout/LineLength: Line is too long. [133/120]

github-actions · 2023-09-18T11:31:44Z

app/models/concerns/attachment_jcamp_aasm.rb

      jcamp_att
    end
  end

  def edit_process(is_regen, orig_params)
    params = build_params(orig_params)
-    tmp_jcamp, tmp_img, arr_jcamp, arr_img, arr_csv, spc_type = generate_spectrum_data(params, is_regen)
+    tmp_jcamp, tmp_img, _, _, arr_csv, arr_nmrium, spc_type, invalid_molfile = generate_spectrum_data(params, is_regen)


Metrics/AbcSize: Assignment Branch Condition size for edit_process is too high. [<14, 22, 6> 26.76/25]

github-actions · 2023-09-18T11:31:44Z

app/models/concerns/attachment_jcamp_aasm.rb

      tmp_files_to_be_deleted.push(*arr_csv)
      delete_related_csv(csv_att)
    end

+    # set_backup
+    unless arr_nmrium.nil? || arr_nmrium.length == 0


Style/NumericPredicate: Use arr_nmrium.length.zero? instead of arr_nmrium.length == 0.

github-actions · 2023-09-18T11:31:47Z

app/models/concerns/attachment_jcamp_aasm.rb

      tmp_files_to_be_deleted.push(*arr_csv)
      delete_related_csv(csv_att)
    end

+    # set_backup
+    unless arr_nmrium.nil? || arr_nmrium.length == 0


Style/ZeroLengthPredicate: Use empty? instead of length == 0.

github-actions · 2023-09-18T11:31:47Z

app/models/concerns/attachment_jcamp_aasm.rb

    jcamp_att
  end

-  def check_invalid_molfile(tmp_img, spc_type, tmp_jcamp)
-    if tmp_img.nil? && spc_type.nil? && tmp_jcamp['invalid_molfile'] == true
+  def check_invalid_molfile(invalid_molfile = false)


Style/OptionalBooleanParameter: Prefer keyword arguments for arguments with a boolean default value; use invalid_molfile: false instead of invalid_molfile = false.

github-actions · 2023-09-18T11:31:47Z

app/models/concerns/attachment_jcamp_aasm.rb

-  def check_invalid_molfile(tmp_img, spc_type, tmp_jcamp)
-    if tmp_img.nil? && spc_type.nil? && tmp_jcamp['invalid_molfile'] == true
+  def check_invalid_molfile(invalid_molfile = false)
+    if invalid_molfile == true


Style/GuardClause: Use a guard clause (return unless invalid_molfile == true) instead of wrapping the code inside a conditional expression.

github-actions · 2023-09-18T11:31:47Z

app/models/concerns/attachment_jcamp_aasm.rb

@@ -268,7 +316,11 @@ def check_invalid_molfile(tmp_img, spc_type, tmp_jcamp)
  end

  def generate_spectrum_data(params, is_regen)
-    tmp_jcamp, tmp_img, arr_jcamp, arr_img, arr_csv, spc_type = Tempfile.create('molfile') do |t_molfile|
+    if params[:ext] == 'nmrium'


Style/IfUnlessModifier: Favor modifier if usage when having a single-line body. Another good alternative is the usage of control flow &&/||.

github-actions · 2023-09-18T11:31:47Z

app/models/concerns/attachment_jcamp_aasm.rb

+      return
+    end
+
+    tmp_jcamp, tmp_img, arr_jcamp, arr_img, arr_csv, arr_nmrium, spc_type, invalid_molfile = Tempfile.create('molfile') do |t_molfile|


Lint/UselessAssignment: Useless assignment to variable - tmp_jcamp. Use _ or _tmp_jcamp as a variable name to indicate that it won't be used.

github-actions · 2023-09-18T11:31:49Z

app/models/concerns/versionable.rb

+
+    result = [] # result data
+    base = {} # track current version data
+    log_data.versions.each do |version|


Metrics/BlockLength: Block has too many lines. [42/25]

github-actions · 2023-09-18T11:31:49Z

app/models/concerns/versionable.rb

+    log_data.versions.each do |version|
+      changes = version.changes # get changes for current version
+      changes_comparison_hash = {} # hash for changes comparison
+      changes.each do |key, value|


Metrics/BlockLength: Block has too many lines. [29/25]

github-actions · 2023-09-18T11:31:49Z

app/models/concerns/versionable.rb

+              o: old_value[key],
+              n: new_value[key],
+              l: label[key],
+              k: kind[key]


Style/TrailingCommaInHashLiteral: Put a comma after the last item of a multiline hash.

github-actions · 2023-09-18T11:31:49Z

app/models/concerns/versionable.rb

+            o: old_value,
+            n: new_value,
+            l: version_label(key), # label for attribute,
+            k: version_kind(key) # kind of attribute (numrange, date, string)


Style/TrailingCommaInHashLiteral: Put a comma after the last item of a multiline hash.

github-actions · 2023-09-18T11:31:49Z

app/models/concerns/versionable.rb

+
+      result << {
+        'k' => version_entity, # record kind (sampe, reaction, ...)
+        'n' => record_name, # record name (uses as default the name attribute but in case the model doesn't have a name field or you want to change it)


Layout/LineLength: Line is too long. [151/120]

PiTrem · 2023-11-14T13:29:02Z

moved to #1253

Allenskywalker92 linked an issue Jul 15, 2022 that may be closed by this pull request

Enhencing versioning feature #780

Closed

3 tasks

Allenskywalker92 force-pushed the 780-enhencing-versioning-feature branch from 7da662c to fedc3a1 Compare July 15, 2022 08:05

Allenskywalker92 requested a review from adambasha0 July 15, 2022 10:32

Allenskywalker92 force-pushed the 780-enhencing-versioning-feature branch from 4bdcf48 to 5e65cf0 Compare July 15, 2022 13:29

ComPlat deleted a comment from adambasha0 Aug 19, 2022

PiTrem changed the base branch from development-5 to v1.4 August 19, 2022 09:15

mschneider85 force-pushed the 780-enhencing-versioning-feature branch from 5e65cf0 to 7543dea Compare November 18, 2022 09:40

PiTrem changed the base branch from v1.4 to development-5 November 22, 2022 11:05

JanCBrammer and others added 5 commits November 29, 2022 15:34

Fix CI status badge (#1059)

dc89e9a

Fix production mode (#1061)

24b414b

dependabot html2pdf version issue (#1056)

b4803f6

* - upgrade html2pdf.js to version 0.10.1 - add process as dev dependency to solve webpack compilation error * move process/browser modules to webpack custom file Co-authored-by: Mehreen <mehreen.mansur>

Activate admin account during seeding (#1060)

93697f0

mschneider85 force-pushed the 780-enhencing-versioning-feature branch from 70c5770 to 7543dea Compare December 1, 2022 08:37

dependabot bot and others added 12 commits December 5, 2022 07:01

Fix link to documentation (#1065)

24af7d2

Current link to docs (https://www.chemotion.net/chemotionsaurus/docs/category/manual) is broken, returns 500.

Fix crashing analyses counter in embedded ResearchPlan within Screen (#…

59e8a8d

…1091)

TasnimMehzabin and others added 11 commits August 24, 2023 11:28

feat: add more reagent to the reaction table reagent dropdown

24bf00c

* add new values to reagents list * add new values to solvents list * add new purification method in Scheme tab of reaction * refactor the code to fix linting issues Refs: #1433 #562

fix: patch citationjs to process doi-sici

e29301f

* build(deps): bump citation-js to 0.6.8 * build: remove library patch in post_install script * feat: patch citation-js library to accept also SICIs Refs: #1486

fix: fixed wrong literatures mapping

81ad5d0

Refs: #1506

fix: ignore predictions when it is null

03b28ce

Co-authored-by: Lan Le <[email protected]> Refs: #1507

feat: update chemspectra frontend to fix bugs

d8ba70f

fix: check the nmrium file before ignore generate

74215eb

feat: update version of chem-spectra-app to handle FL datatype

823c511

fix: cannot read processed data from Bruker Co-authored-by: Lan Le <[email protected]> Refs: #1528

fix: yield percentage error for reactions with decoupled products and…

40bc206

… disable error message for decoupled samples Refs: #1531

mehreenmansur force-pushed the 780-enhencing-versioning-feature branch from 7543dea to a0816e1 Compare September 18, 2023 11:04

github-actions bot reviewed Sep 18, 2023

View reviewed changes

VadimKeller and others added 9 commits September 18, 2023 13:14

dont execute initializers on db create

e23c6f6

Add svg formatter and json

fea76e7

Add revert button to versioned field reset colum information re-create schema update solvent label

Make revert function work

6f90dd5

- Update version list after reverting a change - Fix issue /w big svgs - Make reverting molfile / svg work - Fix merge issues - Replace passing local variables /w using state

resolve merge conflict

937eceb

add version api spec

15ccde9

mehreenmansur force-pushed the 780-enhencing-versioning-feature branch from 0cec773 to 15ccde9 Compare September 18, 2023 11:25

github-actions bot reviewed Sep 18, 2023

View reviewed changes

PiTrem closed this Nov 14, 2023

		@@ -0,0 +1,111 @@
		class Oauth::RadarController < ApplicationController

		@@ -0,0 +1,29 @@
		class ExportCollectionToRadarJob < ActiveJob::Base

780 enhencing versioning feature #800

780 enhencing versioning feature #800

Conversation

Allenskywalker92 commented Jul 15, 2022 • edited by mschneider85 Loading

Allenskywalker92 commented Jul 15, 2022

mschneider85 commented Aug 12, 2022

Allenskywalker92 commented Aug 12, 2022

adambasha0 commented Aug 19, 2022

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Allenskywalker92 commented Jul 15, 2022 •

edited by mschneider85

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