Conversion rate rebased to v1.9.3 #2242
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* chore: rm obsolete files * chore: update nodejs - relax range on LTS * ci: refactor preparation script * ci: update github-ci dockerfile
- re enable DJ delayed modus after models/report_spec - add failure feedback message to spec - DJ logger to stdout in test env
Bumps [rack-contrib](https://github.com/rack/rack-contrib) from 2.3.0 to 2.5.0. - [Release notes](https://github.com/rack/rack-contrib/releases) - [Changelog](https://github.com/rack/rack-contrib/blob/main/CHANGELOG.md) - [Commits](rack/rack-contrib@v2.3.0...v2.5.0) --- updated-dependencies: - dependency-name: rack-contrib dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
* fix: limit attempts for sending welcome mail so that to avoid uncessary sus traffic is the email undeliverable. Define max_attempts as mailer class methods. * chore: remove deused mailer job * fix: avoid sending welcome email to dev seed users
… in report (#1951) display the "Additional information for publication and purification details" for reactions with paragraph structure (similar to the description field) resolve: #1866 Co-authored-by: Tasnim Mehzabin <[email protected]>
…se for admin create user (#1958)
- dep update - nmrium format v3 to v5 - store molfile into nmrium data - dep update - also fix import Co-authored-by: Lan Le <[email protected]>
…#1973) fix method of how parent element of the attachment is found: - take into account that attachments can be associated to other model not only through the container model but also directly with `attachable`. - add tests for attachment in analysis container
Bumps [actionpack](https://github.com/rails/rails) from 6.1.7.7 to 6.1.7.8. - [Release notes](https://github.com/rails/rails/releases) - [Changelog](https://github.com/rails/rails/blob/v7.1.3.4/actionpack/CHANGELOG.md) - [Commits](rails/rails@v6.1.7.7...v6.1.7.8) --- updated-dependencies: - dependency-name: actionpack dependency-type: indirect ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
eventLister added to editor to wait for the editor to be ready before loading the molfile
- db/schema.rb update: `rake db:migrate` on empty pg14 DB
- model annotation: `rake annotate_models`
- db add missing indices:
-- collection-cellline remove potential duplicates before introducing uniq index
with migration test
-- add missing indices for collections_cellline collections_research_plan
…ion (#1915) - `name agnostic` method to get the proper assoicated Collections{Element} for a given AR model through collectable concern or the other way around through the collecting concern update colleciton api accordingly also remove redundant parameter validation - lit api use constant mapping - DRY collection-cellline operations --------- Co-authored-by: PiTrem <[email protected]>
also add adm routine to - restore those - ensure consistent `All` collection content To trigger the recovery or restoration of the locked collections navigate as an Admin to: ` /api/v1/admin/jobs/queue_task?task=collection_restore` Alternately load db/seeds/shared/collections.seed.rb from the rails console.
mv person default profile to profile model
* Add option to force remote display resizing : - Hide the device list on entering focus mode - Show the device list on entering blur mode - Enter blur mode when unhidding the device list - Wait before DeviceList is displayed before resizing the screen - Change label of ScreenResizing Button * Fix jumping viewport when screen is clicked : resolve #2006
* changed methylene chloride to dichloromethane (dcm - methylene chloride)
…1960) * Generalised initializers that load config from a yaml file * Only the validation section is config dependentant. * ensure Rails.application.{structure_editors,ketcher_service} is defined and an instance of ActiveSupport::OrderedOptions, when config/{structure_editors,ketcher_service}.yml: -- is missing or -- is present but nothing defined for the current environment * add minor validation when loading the config yml * should also resolve #1929 when the example file is just copied: proper key in the yml example file --------- Co-authored-by: PiTrem <[email protected]>
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?s=60&v=4){kind=small}
| @@ -614,6 +614,7 @@ def build_sql_reaction_sample(columns, c_id, ids, checkedAll = false) | |||
| # reactions_sample: | |||
| equivalent: ['r_s.equivalent', '"r eq"', 10], | |||
| reference: ['r_s.reference', '"r ref"', 10], | |||
| conversion_rate: ['r_s.conversion_rate', '"r conversion rate"', 10], | |||
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Metrics/ModuleLength: Module has too many lines. [611/100]
| @@ -111,7 +111,7 @@ def create_new_sample(sample, fixed_label) | |||
| :id, :is_new, :is_split, :reference, :equivalent, :position, | |||
| :type, :molecule, :collection_id, :short_label, :waste, :show_label, :coefficient, :user_labels, | |||
| :boiling_point_lowerbound, :boiling_point_upperbound, | |||
| :melting_point_lowerbound, :melting_point_upperbound, :segments | |||
| :melting_point_lowerbound, :melting_point_upperbound, :segments, :conversion_rate | |||
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Metrics/AbcSize: Assignment Branch Condition size for create_new_sample is too high. [<7, 30, 4> 31.06/25]
| @@ -82,6 +82,7 @@ class Import::ImportJson | |||
| # 'r_uuid' => nil, | |||
| # 'r_reference' => nil, | |||
| # 'r_equivalent' => nil, | |||
| # 'r_conversion_rate' => nil, | |||
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Metrics/ClassLength: Class has too many lines. [284/200]
| @@ -374,7 +375,8 @@ def add_to_reaction(klass, el, new_el) | |||
| if new_data && new_data[r_uuid] && new_data[r_uuid]['id'] | |||
| @log['samples'][el_uuid][klass.name] = klass.create( | |||
| sample_id: new_el.id, reaction_id: new_data[r_uuid]['id'], | |||
| reference: ref, equivalent: eq, position: el['r_position'] | |||
| reference: ref, equivalent: eq, position: el['r_position'], | |||
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Metrics/AbcSize: Assignment Branch Condition size for add_to_reaction is too high. [<6, 26, 9> 28.16/25]
| @@ -374,7 +375,8 @@ def add_to_reaction(klass, el, new_el) | |||
| if new_data && new_data[r_uuid] && new_data[r_uuid]['id'] | |||
| @log['samples'][el_uuid][klass.name] = klass.create( | |||
| sample_id: new_el.id, reaction_id: new_data[r_uuid]['id'], | |||
| reference: ref, equivalent: eq, position: el['r_position'] | |||
| reference: ref, equivalent: eq, position: el['r_position'], | |||
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Style/ConditionalAssignment: Use the return of the conditional for variable assignment and comparison.
| @@ -374,7 +375,8 @@ def add_to_reaction(klass, el, new_el) | |||
| if new_data && new_data[r_uuid] && new_data[r_uuid]['id'] | |||
| @log['samples'][el_uuid][klass.name] = klass.create( | |||
| sample_id: new_el.id, reaction_id: new_data[r_uuid]['id'], | |||
| reference: ref, equivalent: eq, position: el['r_position'] | |||
| reference: ref, equivalent: eq, position: el['r_position'], | |||
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Lint/AmbiguousOperatorPrecedence: Wrap expressions with varying precedence with parentheses to avoid ambiguity.
| @@ -333,7 +333,7 @@ def material_hash(material, is_product=false) | |||
| mol: valid_digit(mmol, digit), | |||
| mmol_unit: mmol_unit, | |||
| equiv: valid_digit(s.equivalent, digit), | |||
| molecule_name_hash: s[:molecule_name_hash] | |||
| molecule_name_hash: s[:molecule_name_hash], | |||
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Metrics/ClassLength: Class has too many lines. [606/200]
| @@ -333,7 +333,7 @@ def material_hash(material, is_product=false) | |||
| mol: valid_digit(mmol, digit), | |||
| mmol_unit: mmol_unit, | |||
| equiv: valid_digit(s.equivalent, digit), | |||
| molecule_name_hash: s[:molecule_name_hash] | |||
| molecule_name_hash: s[:molecule_name_hash], | |||
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Metrics/AbcSize: Assignment Branch Condition size for material_hash is too high. [<10, 51, 7> 52.44/25]
| @@ -333,7 +333,7 @@ def material_hash(material, is_product=false) | |||
| mol: valid_digit(mmol, digit), | |||
| mmol_unit: mmol_unit, | |||
| equiv: valid_digit(s.equivalent, digit), | |||
| molecule_name_hash: s[:molecule_name_hash] | |||
| molecule_name_hash: s[:molecule_name_hash], | |||
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Metrics/CyclomaticComplexity: Cyclomatic complexity for material_hash is too high. [8/7]
| @@ -333,7 +333,7 @@ def material_hash(material, is_product=false) | |||
| mol: valid_digit(mmol, digit), | |||
| mmol_unit: mmol_unit, | |||
| equiv: valid_digit(s.equivalent, digit), | |||
| molecule_name_hash: s[:molecule_name_hash] | |||
| molecule_name_hash: s[:molecule_name_hash], | |||
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Metrics/MethodLength: Method has too many lines. [32/30]
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| ElementPermissionProxy.new(current_user, element, user_ids).read_dataset?) | ||
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| if !can_dwnld && (element = @attachment.container&.root&.containable || @attachment.attachable) | ||
| can_dwnld = if element.is_a?(Container) |
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Metrics/BlockNesting: Avoid more than 3 levels of block nesting.
| @message = content_path.read | ||
| @output = markdown(@message) | ||
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| mail(to: @user.email, subject: '[ELN] Welcome to Chemotion.') |
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Rails/I18nLocaleTexts: Move locale texts to the locale files in the config/locales directory.
| @@ -20,8 +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}) | |||
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Layout/LineLength: Line is too long. [182/120]
| end | ||
| self.profile.update_columns(data: data) | ||
| def profile | ||
| super || (new_record? && build_profile ) || create_profile |
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Layout/SpaceInsideParens: Space inside parentheses detected.
| @@ -333,7 +333,7 @@ def material_hash(material, is_product=false) | |||
| mol: valid_digit(mmol, digit), | |||
| mmol_unit: mmol_unit, | |||
| equiv: valid_digit(s.equivalent, digit), | |||
| molecule_name_hash: s[:molecule_name_hash] | |||
| molecule_name_hash: s[:molecule_name_hash], | |||
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| @@ -423,7 +479,7 @@ | |||
| end | |||
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| describe 'POST /api/v1/attachments/thumbnails' do | |||
| pending 'not yet implemented' | |||
| pending | |||
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RSpec/PendingWithoutReason: Give the reason for pending.
… shared collections with read only rights
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rather 1-story 1-commit than sub-atomic commits
commit title is meaningful => git history search
commit description is helpful => helps the reviewer to understand the changes
code is up-to-date with the latest developments of the target branch (rebased to it or whatever) => ⏩-merge for linear history is favoured
added code is linted
tests are passing (at least locally): we still have some random test failure on CI. thinking of asking spec/examples.txt to be commited
in case the changes are visible to the end-user, video or screenshots should be added to the PR => helps with user testing
testing coverage improvement is improved.
CHANGELOG : add a bullet point on top (optional: reference to github issue/PR )
parallele PR for documentation on docusaurus if the feature/fix is tagged for a release