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Enhance import samples for sdf #1364

Merged
merged 4 commits into from
Sep 20, 2023
Merged

Enhance import samples for sdf #1364

merged 4 commits into from
Sep 20, 2023

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adambasha0
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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

@adambasha0 adambasha0 self-assigned this Jun 23, 2023
github-actions[bot]
github-actions bot reviewed Jun 23, 2023
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app/api/chemotion/sample_api.rb Outdated
)
sdf_import.create_samples
return {
sdf: true, message: sdf_import.message,
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Layout/TrailingWhitespace: Trailing whitespace detected.

app/api/chemotion/sample_api.rb Outdated
sdf_import.create_samples
return {
sdf: true, message: sdf_import.message,
status: sdf_import.status,
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Layout/TrailingWhitespace: Trailing whitespace detected.

app/api/chemotion/sample_api.rb Outdated
return {
sdf: true, message: sdf_import.message,
status: sdf_import.status,
error_messages: sdf_import.error_messages,
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Style/TrailingCommaInHashLiteral: Avoid comma after the last item of a hash, unless each item is on its own line.

lib/export/export_excel.rb
@@ -125,6 +125,8 @@ def filter_with_permission_and_detail_level(sample)
regex = /[\[\]()]/
string = sample[column].gsub(regex, '')
string.split(',').join(' - ')
elsif column == 'solvent'
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Metrics/AbcSize: Assignment Branch Condition size for filter_with_permission_and_detail_level is too high. [<13, 29, 22> 38.65/25]

lib/export/export_excel.rb
@@ -125,6 +125,8 @@ def filter_with_permission_and_detail_level(sample)
regex = /[\[\]()]/
string = sample[column].gsub(regex, '')
string.split(',').join(' - ')
elsif column == 'solvent'
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Metrics/CyclomaticComplexity: Cyclomatic complexity for filter_with_permission_and_detail_level is too high. [17/7]

lib/import/import_sdf.rb
@@ -102,7 +129,7 @@ def create_samples
created_by: current_user_id,
molfile: molfile,
molfile_version: babel_info[:molfile_version],
molecule_id: molecule.id
molecule_id: molecule.id,
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Metrics/CyclomaticComplexity: Cyclomatic complexity for create_samples is too high. [59/7]

lib/import/import_sdf.rb
@@ -102,7 +129,7 @@ def create_samples
created_by: current_user_id,
molfile: molfile,
molfile_version: babel_info[:molfile_version],
molecule_id: molecule.id
molecule_id: molecule.id,
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Metrics/MethodLength: Method has too many lines. [126/30]

lib/import/import_sdf.rb
@@ -102,7 +129,7 @@ def create_samples
created_by: current_user_id,
molfile: molfile,
molfile_version: babel_info[:molfile_version],
molecule_id: molecule.id
molecule_id: molecule.id,
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Metrics/PerceivedComplexity: Perceived complexity for create_samples is too high. [64/8]

lib/import/import_sdf.rb
@@ -115,7 +142,7 @@ def create_samples
ActiveRecord::Base.transaction do
attribs = Sample.attribute_names & @mapped_keys.keys
error_messages = []
rows.each do |row|
rows.each_with_index do |row, i|
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Metrics/BlockLength: Block has too many lines. [86/25]

lib/import/import_sdf.rb
@@ -115,7 +142,7 @@ def create_samples
ActiveRecord::Base.transaction do
attribs = Sample.attribute_names & @mapped_keys.keys
error_messages = []
rows.each do |row|
rows.each_with_index do |row, i|
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Metrics/BlockLength: Block has too many lines. [78/25]

github-actions[bot]
github-actions bot reviewed Jun 23, 2023
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spec/api/chemotion/sample_api_spec.rb Outdated
@@ -281,8 +281,8 @@
"density": 'Test',
"decoupled": 'f',
"molarity": '900sdadsad',
"melting_point": 'test900',
"boiling_point": 'test1000',
"melting_point": '900',
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Lint/SymbolConversion: Unnecessary symbol conversion; use melting_point: instead.

spec/api/chemotion/sample_api_spec.rb Outdated
@@ -281,8 +281,8 @@
"density": 'Test',
"decoupled": 'f',
"molarity": '900sdadsad',
"melting_point": 'test900',
"boiling_point": 'test1000',
"melting_point": '900',
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Style/QuotedSymbols: Prefer single-quoted symbols when you don't need string interpolation or special symbols.

spec/api/chemotion/sample_api_spec.rb Outdated
"melting_point": 'test900',
"boiling_point": 'test1000',
"melting_point": '900',
"boiling_point": '1000',
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Lint/SymbolConversion: Unnecessary symbol conversion; use boiling_point: instead.

spec/api/chemotion/sample_api_spec.rb Outdated
"melting_point": 'test900',
"boiling_point": 'test1000',
"melting_point": '900',
"boiling_point": '1000',
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Style/QuotedSymbols: Prefer single-quoted symbols when you don't need string interpolation or special symbols.

github-actions[bot]
github-actions bot reviewed Jun 23, 2023
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lib/import/import_sdf.rb
@@ -2,9 +2,9 @@

require 'charlock_holmes'

class Import::ImportSdf
class Import::ImportSdf < Import::ImportSamples
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Metrics/ClassLength: Class has too many lines. [252/200]

lib/import/import_sdf.rb
@@ -102,7 +129,7 @@ def create_samples
created_by: current_user_id,
molfile: molfile,
molfile_version: babel_info[:molfile_version],
molecule_id: molecule.id
molecule_id: molecule.id,
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Metrics/AbcSize: Assignment Branch Condition size for create_samples is too high. [<64, 216, 68> 235.3/25]

lib/import/import_sdf.rb
@@ -102,7 +129,7 @@ def create_samples
created_by: current_user_id,
molfile: molfile,
molfile_version: babel_info[:molfile_version],
molecule_id: molecule.id
molecule_id: molecule.id,
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Metrics/CyclomaticComplexity: Cyclomatic complexity for create_samples is too high. [60/7]

lib/import/import_sdf.rb
@@ -102,7 +129,7 @@ def create_samples
created_by: current_user_id,
molfile: molfile,
molfile_version: babel_info[:molfile_version],
molecule_id: molecule.id
molecule_id: molecule.id,
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Metrics/MethodLength: Method has too many lines. [127/30]

lib/import/import_sdf.rb
@@ -102,7 +129,7 @@ def create_samples
created_by: current_user_id,
molfile: molfile,
molfile_version: babel_info[:molfile_version],
molecule_id: molecule.id
molecule_id: molecule.id,
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Metrics/PerceivedComplexity: Perceived complexity for create_samples is too high. [65/8]

spec/api/chemotion/sample_api_spec.rb
"name": 'name'
}]
inchikey: 'DTHMTBUWTGVEFG-DDWIOCJRSA-N',
molfile: Rails.root.join('spec', 'fixtures', 'mf_with_data_01.sdf').read,
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Rails/FilePath: Prefer Rails.root.join('path/to').

spec/api/chemotion/sample_api_spec.rb
}]
inchikey: 'DTHMTBUWTGVEFG-DDWIOCJRSA-N',
molfile: Rails.root.join('spec', 'fixtures', 'mf_with_data_01.sdf').read,
description: "MOLECULE_NAME\n(R)-Methyl-2-amino-2-phenylacetate hydrochloride ?96%; (R)-(?)-2-Phenylglycine methyl ester hydrochloride\n\nSAFETY_R_S\nH: 319; P: 305+351+338\n\nSMILES_STEREO\n[Cl-].COC(=O)[C@H](N)c1ccccc1.[H+]\n",
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Layout/LineLength: Line is too long. [241/120]

spec/api/chemotion/sample_api_spec.rb
@@ -610,17 +611,17 @@
boiling_point_lowerbound: 100,
melting_point_upperbound: 200,
melting_point_lowerbound: 200,
molfile: File.read(Rails.root + 'spec/fixtures/test_2.mol'),
molfile: File.read("#{Rails.root}/spec/fixtures/test_2.mol"),
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Rails/FilePath: Prefer Rails.root.join('path/to').

spec/api/chemotion/sample_api_spec.rb
IO.read(File.join(
Rails.root, 'spec', 'fixtures', 'sample_update_1_params.json'
))
Rails.root.join('spec', 'fixtures', 'sample_update_1_params.json').read,
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Rails/FilePath: Prefer Rails.root.join('path/to').

spec/api/chemotion/sample_api_spec.rb
headers: { 'CONTENT_TYPE' => 'application/json' }
)
end.to change { s2.analyses.first.children.count }.by 0
params: sample_upd_1_params.to_json,
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Lint/AmbiguousBlockAssociation: Parenthesize the param change { s2.analyses.first.children.count } to make sure that the block will be associated with the change method call.

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LCOV of commit f52fa75 during Continuous Integration #1162

Summary coverage rate:
  lines......: 60.6% (12361 of 20386 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@PiTrem PiTrem added this to the v1.8 milestone Jul 11, 2023
@adambasha0 adambasha0 force-pushed the enhance_import_samples_for_sdf branch from f52fa75 to 6d5cfad Compare July 11, 2023 14:21
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LCOV of commit 6d5cfad during Continuous Integration #1279

Summary coverage rate:
  lines......: 59.8% (12399 of 20740 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@FabianMauz FabianMauz self-requested a review August 22, 2023 07:49
FabianMauz
FabianMauz suggested changes Aug 23, 2023
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While testing the import with various sdf files i noticed some issues/bugs:

  1. The ui for the preview is to small, i can not see every property
    20230823_import_overview_table

  2. when importing i got some strange sample svg images
    20230823_benzene_import_on_PR

Using the same sdf file on the uncharted results in
20230823_benzene_import_on_uncharted

app/api/chemotion/sample_api.rb
@@ -74,36 +74,19 @@ class SampleAPI < Grape::API
# Create a temp file in the tmp folder and sdf delayed job, and pass it to sdf delayed job
extname = File.extname(params[:file][:filename])
if extname.match(/\.(sdf?|mol)/i)
sdf_import = Import::ImportSdf.new(file_path: params[:file][:tempfile].path,
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Suggestion: Extract the logic into separate methods:
line 76 - 90 -> importFromMolFile ( )
line 91 - 120 -> importFromXlsCsv ( ) -> here you could even split it again in immediatelyImport ( ) and jobBasedImport ( )

app/api/chemotion/sample_api.rb
file_name: file['filename'],
file_path: tmp_file_path,
}
ImportSamplesJob.perform_later(parameters)
{ status: 'in progress', message: 'Importing samples in background' }
end
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What happens, if it is not Sdf, mol, csv or xls format. I think it will go into the xls/csv branch and crash somewhere there. Maybe a rescue needed ?

Edited: i saw that in the import_samples_job.rb there is a case statement which checks if format is .xlsx or .sdf and otherwise throws and error.

app/packs/src/fetchers/SamplesFetcher.js Outdated
@@ -184,14 +184,21 @@ export default class SamplesFetcher {
}).then((response) => {
return response.json();
}).then((json) => {
for (let i = 0; i < json.error_messages.length; i++) {
if (Array.isArray(json.error_messages)) {
for (let i = 0; i < json.error_messages.length; i++) {
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maybe with a lamba for better readability?
json.error_messages.forEach( (errorText)=> NotificationActions.add({message: errorText, level: 'error', autoDismiss: 10});)

lib/export/export_sdf.rb Show resolved Hide resolved
lib/export/export_table.rb Outdated

return nil if solvent_hash.nil?

solvent_hash[0]&.fetch('label', nil)
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is it correct that only the first solvent is used?

lib/import/import_sdf.rb
@@ -2,9 +2,9 @@

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General observation:

  • It would make the file much more readable if the large context blocks e.g. 142 - 240 would be splitted into separate methods with self explaining names
  • opening a transaction for every single sample seems to be a heavy load for the DB. Maybe separate the extracting part from the file to a intermediate format, then have a validation on that format and at the end only import the valid data in one transaction.

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FabianMauz approved these changes Sep 1, 2023
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Css seems to be fixed, had a talk with Adam about some comments.

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github-actions bot commented Sep 1, 2023

LCOV of commit e3949c5 during Continuous Integration #1676

Summary coverage rate:
  lines......: 59.7% (12439 of 20821 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@adambasha0
refactor export of sample solvent to export solvent name(not the solv…
593623e 
…ent hash)- refactor export samples for sdf for melting and boiling points columns and write import sample job for sdf format and refactor and write import samples jobs spec tests for sdf format
@adambasha0
fix typo & refactor boiling and melting points params in sample_api_s…
cf7ed94 
…pec test
@adambasha0
add density column to import samples with sdf format and refactor sam…
fa695bf 
…ple_api_spec file
@adambasha0
improve extract solvent and other functions for sdf export
7785dbe
FabianMauz
FabianMauz approved these changes Sep 8, 2023
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all ok, had a talk with Adam about some minor ideas

@adambasha0 adambasha0 force-pushed the enhance_import_samples_for_sdf branch from e3949c5 to 7785dbe Compare September 8, 2023 08:58
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LCOV of commit 7785dbe during Continuous Integration #1705

Summary coverage rate:
  lines......: 59.7% (12439 of 20823 lines)
  functions..: no data found
  branches...: no data found

Files changed coverage rate: n/a

@PiTrem PiTrem merged commit dc4283b into main Sep 20, 2023
2 checks passed
mekkyz pushed a commit that referenced this pull request Sep 21, 2023
@adambasha0 @mekkyz
feat: Enhance import samples for sdf
cd20e6e 
* refactor export of sample solvent to export solvent name(not the solvent hash)- refactor export samples for sdf for melting and boiling points columns and write import sample job for sdf format and refactor and write  import samples jobs spec tests for sdf format

* fix typo & refactor boiling and melting points params in sample_api_spec test

* add density column to import samples with sdf format and refactor sample_api_spec file

* improve extract solvent and other functions for sdf export

Ref: #1364
PiTrem added a commit that referenced this pull request Feb 6, 2024
@PiTrem
merge squash main / fix btn conflict
f976908 
Squashed commit of the following:

commit 97cf66f0ecd7427a4960d6b2d5c078a5a3e3b6e0
Author: Mehreen Mansur <[email protected]>
Date:   Thu Feb 1 15:21:06 2024 +0100

    fix: export research plan error on docx format (#1718)

    arg not accepted since gem upd  (ComPlat/chemotion_ELN@f0d6f7b)

    also fix error on table input

commit d78f48e89cc94cdd20c88f4bc47a347e46c8b094
Author: Mehreen Mansur <[email protected]>
Date:   Thu Feb 1 11:28:37 2024 +0100

    feat: add helpdesk link in header (#1713)

commit 6a6c3aa6a16a849ed0fd748df704f3b814df4fb4
Author: f-idiris <[email protected]>
Date:   Thu Feb 1 11:08:29 2024 +0100

    fix: nmrium  missing 'close with save' button  in research plan

    Refs: #1715

commit 8a257e2489a230406c57bf82faab347465c61d31
Author: Adam Basha <[email protected]>
Date:   Thu Feb 1 11:07:07 2024 +0100

    fix: focus lost on input bug for melting & boiling points fields

    Refs: #1716

commit dc3203f04edfd2eb565ac9ba836aba70afa719cd
Author: PiTrem <[email protected]>
Date:   Wed Jan 31 15:08:22 2024 +0100

    fix: dfg logo resource in README.md (#1710)

    * fix: dfg logo resource in README.md

    * Update README.md

commit 3097ba2006352109b247d6301ae8a2258060cc15
Author: PiTrem <[email protected]>
Date:   Wed Jan 31 13:28:09 2024 +0100

    feat: Inbox device folders named with the device fullname

    (previously only firstname was used)

    db migration to rename Inbox-device folders

    Refs:  #1709

commit 1f3d0b52353eb4a2f0cbf7c4c51ddd1eceb6e067
Author: Pei Chi Huang <[email protected]>
Date:   Wed Jan 31 12:13:53 2024 +0100

    feat: filter jdx files to be processed by converter-app

    prevent chemspectra generated jdx files to be processed by chemotion-converter-app jdx reader

    Co-authored-by: Chia-Lin Lin <[email protected]>

    Refs:  #1712

commit 5daa9eb5e84fa244e32de29615316739233f9724
Author: f-idiris <[email protected]>
Date:   Wed Jan 31 09:28:55 2024 +0100

    feat: enable nmrium in read only collection (#1708)

commit 587ee7e1248c10ea83a35bfb7a6c89eb3a75f32e
Author: Adam Basha <[email protected]>
Date:   Wed Jan 31 08:46:50 2024 +0100

    feat: input field  for general remarks on all sample analyses

    Refs: #1696

commit affe293585209b7ff0bdac024f2a4990a23e693b
Author: Pei Chi Huang <[email protected]>
Date:   Tue Jan 30 16:46:19 2024 +0100

    fix: data cannot be removed from segment of element

    https://github.com/LabIMotion/labimotion/releases/tag/v1.1.2

    Co-authored-by: Chia-Lin Lin <[email protected]>

    Refs: #1711

commit d6f881903c5300129b6a44dfbd7d41acce183b29
Author: f-idiris <[email protected]>
Date:   Tue Jan 30 16:22:56 2024 +0100

    feat: label detector in SEC spectra

    *  label detector in SEC spectra

    *  update chemspectra to v1.1.1

    Refs:  #1691

commit c83ed704d6eb3232bc0a841a91b69672e7256042
Author: Christian Buggle <[email protected]>
Date:   Tue Jan 30 08:39:41 2024 +0100

    feat: Add models VesselTemplate, Vessel, CollectionsVessel

    * Add models VesselTemplate, Vessel, CollectionsVessel, Minimal models as required as a common base for the upcoming ReactionProcessEditor and upcoming features in ELN

    * Add migration and models for VesselTemplates, Vessel, CollectionsVessel.

    * Add gem ‘shoulda-matchers’ in environment :test.

    * Add shared_example :acts_as_paranoid_soft_deletable_model, include in the specs of all affected models.

    * Enable extension `pg_crypto` in schema.rb as this should be there from earlier migration 20220712100010_add_segment_klass_identifier.rb.

    * Use well defined ORD constants for vessel_type, material_type.
    * Add created vessel to user’s collection.

    * Make idempotent, do not run if vessel name exists.

    * Add weight, barcode, qrcode to Vessels

    * Add weight_amount, weight_unit to VesselTemplate, delegate in Vessel.

    * seeds for VesselTemplates & Vessels

    ---------

    Co-authored-by: nh9378 <[email protected]>

    Refs: #1548

commit 318fd345d60a2d0419bcf0faf5c2ce058f4ad8af
Author: TasnimMehzabin <[email protected]>
Date:   Tue Jan 30 08:35:06 2024 +0100

    feat: sort the device list by name in command_n_control (#1707)

    Co-authored-by: Tasnim Mehzabin <[email protected]>

commit 4ac32c73d2d004962afca7e4fe113ff12e667b9d
Author: Pei Chi Huang <[email protected]>
Date:   Thu Jan 25 17:32:34 2024 +0100

    feat: upgrade converter to v1.2.0 (#1704)

commit 89db312b00f4e3cd3b532c2347411a220f2e56c5
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Wed Jan 24 12:36:22 2024 +0100

    chore: Bump puma from 5.6.7 to 5.6.8 (#1679)

    Bumps [puma](https://github.com/puma/puma) from 5.6.7 to 5.6.8.
    - [Release notes](https://github.com/puma/puma/releases)
    - [Changelog](https://github.com/puma/puma/blob/master/History.md)
    - [Commits](https://github.com/puma/puma/compare/v5.6.7...v5.6.8)

    ---
    updated-dependencies:
    - dependency-name: puma
      dependency-type: direct:production
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit f0d6f7b90e114eb999d81918fa350ea65e9eaadd
Author: Christian Buggle <[email protected]>
Date:   Wed Jan 24 11:22:17 2024 +0100

    chore: missing constant MIME::Types

    * Fix missing constant MIME::Types

    * Add gem ‘mime-types’ to Gemfile:

     in preparation to  ketcherails update: latest ketcherrails which no longer carries a dependency to `paperclip ->  mime-types`.

    * patch farraday

    Refs: #1660

commit 29a861853b3313d096f46613f410bf9a76a65ad9
Author: Mostafa Mekky <[email protected]>
Date:   Wed Jan 24 10:30:07 2024 +0100

    fix(UI): sample entry label alignment (#1693)

commit d60d9f7958b14bca76266e763b94d8663c7e4e49
Author: Adam Basha <[email protected]>
Date:   Wed Jan 24 10:27:08 2024 +0100

    fix: amount change of a reaction product from the sample properties tab

    * fix: bug for amount change of a reaction product sample from sample properties tab, does not render the change in the reaction scheme after saving sample change

    * assignAmountType when sample benlongs to reaction

    Refs: #1692

commit 5eedcef0bafff684abda425d9a297beac5968bb1
Author: Lan Le <[email protected]>
Date:   Wed Jan 24 09:21:27 2024 +0100

    feat: update react-spectra-editor to display theoretical mass value

    Co-authored-by: Lan Le <[email protected]>
    Refs: #1675, https://github.com/ComPlat/react-spectra-editor/pull/186

commit c69bbf00bb5a8c9bd6614eb979f1293a172ecbc8
Author: Jan C. Brammer <[email protected]>
Date:   Wed Jan 24 09:03:36 2024 +0100

    feat: Add `variations` attribute to reaction report settings (#1697)

commit e51e89d8d3f960aee5bcfdc989cb061198063af3
Author: Adam Basha <[email protected]>
Date:   Tue Jan 23 08:56:54 2024 +0100

    feat: add sample inventory label counter

    add inventory model and inventory label feature

    Refs: #1581

commit dffea5bb8219ed49ce2c6cc4f2b82c5e1e1d28c1
Author: Jan C. Brammer <[email protected]>
Date:   Tue Jan 23 08:52:55 2024 +0100

    refactor: extract` SpectraEditorButton` to dedicated component

    * Extract` SpectraEditorButton`  to dedicated component

    * Pass missing `element` parameter to `SpectraEditorButton`

    Refs: #1664

commit 41928e8fe5fbd4b62b169a31e63106c639682ea2
Author: Mostafa Mekky <[email protected]>
Date:   Tue Jan 23 08:51:29 2024 +0100

    feat: group analysis attachments

    attachments are grouped according to their original/processed status

    added better thumbnail preview

    Refs: #1674

commit f8362ac9aa69fc49f4a19ab8e8bd0f25e5ab6d57
Author: Jan C. Brammer <[email protected]>
Date:   Tue Jan 23 08:48:39 2024 +0100

    fix(UI): show Tooltip on + button in reaction-variations tab (#1694)

commit 16f75929f91b3f233b4c3253db927ad7940eaef0
Author: Pei Chi Huang <[email protected]>
Date:   Thu Jan 18 15:07:30 2024 +0100

    fix(int): zip upload

    Co-authored-by: Chia-Lin Lin <[email protected]>

    Refs: #1690, #1688

commit 9a765180670bd9c737630ac31668786adf6026aa
Author: Lan Le <[email protected]>
Date:   Thu Jan 18 09:52:35 2024 +0100

    test: fix stub request in spectra jdx test

    Co-authored-by: Lan Le <[email protected]>
    Refs: #1689, #1596

commit 1a93cf52ceac1eed19d2ffc50c62c4528531df0e
Author: Pei Chi Huang <[email protected]>
Date:   Mon Jan 15 15:51:43 2024 +0100

    feat: converter metadata  added to dataset download (#1688)

    Dataset-xls improvement - more information is provided in the Description sheet.

    See the documentation https://www.chemotion.net/docs/labimotion/guides/user/datasets/download

    Co-authored-by: Chia-Lin Lin <[email protected]>

commit 69ad0a9ad183a9d614489a1ea38a47f82895b6b1
Author: PiTrem <[email protected]>
Date:   Mon Jan 15 13:13:29 2024 +0100

    refactor: dry schmooze tools (#1684)

    common input parser for quill-to-html and quill-to-plain-text

    now handle empty delta to prevent (db/migration) errors
    ```
         Schmooze::JavaScript::TypeError:
           only `insert` operations can be transformed!
    ```

commit 7097d40324fe40145ddaca8819e9e135b9eff236
Author: Lan Le <[email protected]>
Date:   Mon Jan 15 11:12:20 2024 +0100

    chore: update runner - fix text (#1683)

    * test: fix mock api for jcamp process

    * test: test rubocop action to use ruby  3.3

    * chore: npx browserslist@latest --update-db

    * chore: yarn-audit-fix

    * chore: upd gitignore

    * chore: update CHANGELOG v1.8.1

    * chore: update db/schema.rb

    ---------

    Co-authored-by: Lan Le <[email protected]>
    Co-authored-by: PiTrem <[email protected]>

commit 5bee5403e369abd63a2fcb64ff7e46dcef98a9fd
Author: Jan C. Brammer <[email protected]>
Date:   Wed Jan 10 15:47:09 2024 +0100

    fix: temperature conversion in reaction

    Refs: #1680

commit 4c7b2ff43a2025c7a92f4319b3d1181366e94010
Author: Mostafa Mekky <[email protected]>
Date:   Wed Jan 10 15:45:24 2024 +0100

    fix: remove duplicate user label and center the share button (#1682)

commit 234fb88b0b6a28d7656b828ffa673764b18daf43
Author: Fabian Mauz <[email protected]>
Date:   Wed Jan 10 09:08:50 2024 +0100

    fix: tests for searching cell lines (#1678)

commit a0c1b34399cc31fccd0263d1c7d194fb8dad4189
Author: f-idiris <[email protected]>
Date:   Wed Jan 10 09:01:01 2024 +0100

    feat: Table of data types and chemspectra layouts in the ELN Admin

    * feat: Add chemspectra admin for updating data type

    * datatype list managed on the ELN with default values from chemspectra is passed to chemspectra as arg.

    Refs: #1574

commit f8edcd6a61cae163d04a129f91ffe76ca6dc4fa3
Author: Fabian Mauz <[email protected]>
Date:   Mon Jan 8 10:28:13 2024 +0100

    feat: add new element cell line

    cell-line as a stand-alone element :
    user can manage cell-line samples in their collections.

    add 2 models: CelllineSample and CelllineMaterial (belongs to CelllineSample)

    export/import collection  with cell-lines

    bioassay ontology  for cell line analysis

    search of cell line by material/sample name

    Refs: #1582

commit 0be3cd98440476b86db207021f5675f74da3ca60
Author: Beate Quednau <[email protected]>
Date:   Fri Jan 5 15:20:40 2024 +0100

    feat: extend search

    * Add search modal

    * Add toggable panel for search and result at search modal forms

    * Add search result tab lists

    * Add search result tab content with pagination

    * Add advanced search form fields

    * Add element list filter to search result

    * Add handle safe for advanced search and ketcher

    * Add handle refind, adopt result

    * Add clear search and tab results, Set tab index for tab with results

    * Add order and group by molecule to search results

    * Clear search when clicking on collection

    * Add search by ids for search result tab pages

    * Add alert to remove search result

    * Add basic element selection for advanced search

    * Add search queries for reactions, wellplates and screens, and research plans

    * Add publication search

    * Add basics for generic element search

    * Add hr to generic element search for testing deployment

    * Add more search fields for reactions and screens

    * Add temperature and duration to reaction search fields

    * Add readout titles at wellplate search

    * Add quill to plain text and additional plain text field for description fields

    * Add description fields to search

    * Remove old advanced  and structure search, Remove old generic search, cleanup

    * Add use cases for advanced search, search by ids, structure search

    * Add input-group, formula, table fields to detail search

    * Add better error messages

    * Add search results store and simple search results

    * Simplify visibility of search modal with mobx store

    * Add plain text content to containers, refactore fieldsByTabs

    * Add solvent fields to sample search

    * Add unit tests for advanced, structure and by_ids search

    * Add cypress test and identificator for search modal

    * Add klasses.json to gitignore

    * Add more descriptions for readme-dev

    * Fix ketcher rails search

    * Fix advanced search with multi search fields

    * Fixes for generic elements

    * Fix base fetcher for generic elements

commit d7144d433d62287702f6bd83ae765a2f261d6b9f
Author: TasnimMehzabin <[email protected]>
Date:   Thu Dec 21 10:35:36 2023 +0100

    fix: attached research_plans in screens not being imported from collection

    * fix: attached research_plans in screens not being imported from collection
    wellplates not being imported from collection

    * style: rubocop

    ---------

    Co-authored-by: Tasnim Mehzabin <[email protected]>
    Refs: #1671

commit cc3930d079d7e958f158edc860d0626df5876660
Author: Mostafa Mekky <[email protected]>
Date:   Wed Dec 20 11:36:15 2023 +0100

    feat: Unified attachment list

    enhancing attachment list:

    applying new attachment list to Datasets, research plan and well-plate attachments

    * feat: sorting feat by name, date ( hide sorting functions if no attachments)

    * enabling style prop on component

    * refactor: Dataset Modal Redesign

    * refactor: converting inline styles to scss

    * Style: cleaner code and linking to new css classes

    * dataset modal discarding logic

    * unifying edited image warning text

    * style: eslint fixes and css enhancements

    * feat: strike attachment name when deleted

    * Removed discard btn for 1.9.0

    ---------

    Refs: #1608

commit 324bc372f2acc34712a441ed045f4f3bda77994a
Author: Lan Le <[email protected]>
Date:   Wed Dec 20 10:53:30 2023 +0100

    fix: remove original data from nmrium data before storing it

    Co-authored-by: Lan Le <[email protected]>
    Refs: #1661

commit 63c4e32e0441656081e13088be6ce63b5af101d0
Author: PiTrem <[email protected]>
Date:   Wed Dec 20 06:21:01 2023 +0100

    fix: camelcasing attributes for proper display of SVGs

    * fix: camelcasing attributes for proper display of svgs

    due to the scrubber library lowercasing all attribute names some properties
    are not rendered in the browser.

    In this case beads with a gradient  in molecule, sample and reaction
    were not displayed in browser and were also missing after conversion in png in doc report.

    (successiv gsub benchmarked as faster than gsub with regex and a dict)

    * upd yarn.lock

    Refs:  #1670

commit 15768e0b30894011397285e350bcd3ad4c8bf902
Author: Lan Le <[email protected]>
Date:   Wed Dec 20 06:00:40 2023 +0100

    feat: add chemspectra with ref peaks (#1596)

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

commit 589e8b8bc46bc1d17c19f2af978b5368dcef0ad5
Author: Lan Le <[email protected]>
Date:   Wed Dec 20 05:52:53 2023 +0100

    fix(spectra): react-spectra-editor upd to correct molecule display with svg zoom pan

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

    Refs: #1656, https://github.com/ComPlat/react-svg-file-zoom-pan/pull/44

commit df1a75b92b4f2ad3786a63810720dc81f152d080
Author: Johannes Haubold <[email protected]>
Date:   Wed Dec 13 12:36:05 2023 +0100

    chore: Improve Dev Setup by autorecognizing the installed tool versions (#1665)

commit a1fdf19339ff1583779152af3e9f641b666e4452
Author: Mostafa Mekky <[email protected]>
Date:   Tue Dec 12 08:21:01 2023 +0100

    fix(UX): molecule title layout and element table header responsiveness

    * spacing at sample header

    * responsive element table header

    *  eslint

    * remove gray color

    * remove unneeded margin right

    Refs: #1650, #1646

commit 1d259fadb8a17f34087dcc131adc774959a212c8
Author: Mehreen Mansur <[email protected]>
Date:   Tue Dec 12 08:09:39 2023 +0100

    fix: si-spectra report generation to work even without preview

    * serialize data for spectra si report on backend

    * add spectra report thumbnail image preview

    * update spectra worker method

    * update attachment api

    ---------

    Co-authored-by: Mehreen <mehreen.mansur>

    Refs:  #1654, #1642

commit 016eab42b1ce350322285e1d8b3879678eb64d35
Author: TasnimMehzabin <[email protected]>
Date:   Tue Dec 12 07:58:20 2023 +0100

    feat: add the option to change the inbox sizing

    * feat: add the option to change the inbox sizing
    make the default inbox sizing smaller to col-md-4

    * feat: hide the datetime when inbox size is set to 'Small'
    change small inbox size to col-md-2
    change css for sort button in inbox modal
    modify the info message in the inbox for the sort button

    ---------

    Co-authored-by: Tasnim Mehzabin <[email protected]>
    Co-authored-by: mekkyz <[email protected]>

    Refs:  #1645

commit b8cde5288c6829bce1f3accccf6d0f6dd8b8b1b1
Author: TasnimMehzabin <[email protected]>
Date:   Thu Dec 7 08:46:27 2023 +0100

    test: fix test with deviceBox sorting in inbox

    Co-authored-by: Tasnim Mehzabin <[email protected]>

    Refs: #1657 , #1446

commit fed53fa6568642af069377ebe4ce4b78d70c37b9
Author: TasnimMehzabin <[email protected]>
Date:   Tue Dec 5 15:55:56 2023 +0100

    feat: sorting option for datasets and attachments in the inbox by creation-time or name

    * feat: modify the sorting in the inbox based on user selection (name/creation time)
    add test codes
    prevent the deviceBox from being closed when ordering is changed

    deviceBox not to change with the sorting options. They will always be fixed and sorted by the name
    unsorted files are sorted with the selected sorting
    attachments within the datasets are sorted with the selected sorting
    the sorting icon is modified
    the default inbox sizing is made smaller to col-md-4
    tooltip texts are directed downward

    ---------

    Co-authored-by: Tasnim Mehzabin <[email protected]>

    Refs: #1446

commit 3752367b14fadb8f090b62e0c63a97bb3990c53e
Author: Lan Le <[email protected]>
Date:   Tue Dec 5 15:28:23 2023 +0100

    fix(spectra): order of J value

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

    Ref: #1649, https://github.com/ComPlat/react-spectra-editor/pull/179

commit a87201224d7a2cc88ab9f75342c308ad3295dd8c
Author: Lan Le <[email protected]>
Date:   Tue Dec 5 15:26:15 2023 +0100

    fix(spectra): correctly trigger action spinner when saving peaks to avoid race condition

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

    Refs: #1651

commit d503a4c5fa135b808bb80c77ef82d310cb40d2e8
Author: TasnimMehzabin <[email protected]>
Date:   Wed Nov 29 14:34:32 2023 +0100

    fix: reaction sort column value not being persistent for updated_at column

    Co-authored-by: Tasnim Mehzabin <[email protected]>

    Refs: #1643

commit 97fcdd69aea585f94ac6ff62103968f8c519f181
Author: Mehreen Mansur <[email protected]>
Date:   Wed Nov 29 12:47:59 2023 +0100

    feat: show research plan links in reaction (#1575)

    * add research plans linked to reaction

    * update research plan api

    ---------

    Co-authored-by: Mehreen <mehreen.mansur>

commit baadf31dc2aea0407de05cb188d7e2a15ccd306d
Author: Lan Le <[email protected]>
Date:   Wed Nov 29 11:10:24 2023 +0100

    fix: update chemspectra client to prevent crash on CV layout

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

    Refs: #1637, https://github.com/ComPlat/react-spectra-editor/pull/177

commit 93f8dce78cd647cec3adb653fb7093cadecc1e74
Author: Fabian Mauz <[email protected]>
Date:   Wed Nov 29 11:07:12 2023 +0100

    fix: collection management right click on the add button to not drag things around

    * fix: made root collection undraggable in MyCollections

    * style: changed css style of root collections

    * fix: made root collection in MySharedCollections undraggable

    * fix: made root collection in Shared-and SyncronizedWithMe  undraggable

    * fix: made root collection in CollectionTabs  undraggable

    * style: add some space left to the tree

    * style: add active marking also to root collection

    * fix: suppress drag with root buttons at MyCollections

    * fix: suppress drag with root buttons at MySharedCollections

    refs: #1639, #670

commit 5e3d9814e0761b6617307f961c9f5244033fb4f4
Author: Adam Basha <[email protected]>
Date:   Fri Nov 24 10:40:14 2023 +0100

    feat: add volume field in inventory tab (#1613)

    * add volume field in inventory tab

    * fix: apply conditional check for p-statements in chemicalTab

    * fix: verify fetched pictograms from merck

commit cf7e0b077ab652a3f02ea7c7969b6c6b629baed1
Author: StarmanMartin <[email protected]>
Date:   Tue Nov 21 22:32:04 2023 +0100

    feat: Changed Mail collector rules

    * Changed Mail collector rules:
    Attachment e-mails...
     - can be sent to multiple chemotion instances
     - can be sent to chemotion user in 'cc' or 'to'. The e-mail addresses in to and cc are treated equally
     - can be sent to different e-mails. All emails in "cc" or "to" belonging to a registered user will trigger the creation of an attachment. All non-registered e-mails are ignored.

    Additionally, if an e-mail throws an error the collector keeps running. -> mailcollector line 25

    * style: rubocop -A

    Refs: #1566

commit fa19ed25769df52c273037f4eb291c41a4322076
Author: PiTrem <[email protected]>
Date:   Tue Nov 21 21:53:06 2023 +0100

    chore: upd node engine for dev container (#1635)

    * chore: upd node engine for dev container

    * feat: enable sentry monitoring for delayed_job

    * chore: upd dockerignore

    * ci: update runner image

    * ci: move faker to global group of Gems to allow user seedings in stage env

commit 9876a63639436999eb9975e5a10541acb9a72b78
Author: Adam Basha <[email protected]>
Date:   Mon Nov 20 17:05:02 2023 +0100

    fix: allow import of molecule_name on sample import for xslx format

    * fix: allow import of molecule_name on sample import for xslx format

    * add spec test for importing molecule names on sample import

    Refs: #1598

commit b7f13f4179ad0cf5e31ada00780faa59e59f427c
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Mon Nov 20 16:32:30 2023 +0100

    chore: Bump rmagick from 5.0.0 to 5.3.0

    Bumps [rmagick](https://github.com/rmagick/rmagick) from 5.0.0 to 5.3.0.
    - [Changelog](https://github.com/rmagick/rmagick/blob/main/CHANGELOG.md)
    - [Commits](https://github.com/rmagick/rmagick/commits)

    ---
    updated-dependencies:
    - dependency-name: rmagick
      dependency-type: direct:production
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

    Refs: #1609

commit e3b90c636b0b1cd419f31b59ea591abafb9c9c50
Author: Lan Le <[email protected]>
Date:   Mon Nov 20 16:30:21 2023 +0100

    fix(spectra): Add/remove multiplicity peak buttons(#1630)

    update react-spectra-editor to v1.0.0-rc20

    https://github.com/ComPlat/react-spectra-editor/pull/175

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

    Refs: 1630

commit 8b8690d8646a9707ee8e40026b213cebbbbfa1f7
Author: Lan Le <[email protected]>
Date:   Mon Nov 20 16:17:20 2023 +0100

    fix(spectra): remove blank line when saving peak

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

    Refs: #1629

commit e559183511e644df48ec363da9186dcc36f6eb69
Author: Pei Chi Huang <[email protected]>
Date:   Mon Nov 20 15:56:32 2023 +0100

    feat: upgrade-converter-to-v1.1.1

    https://github.com/ComPlat/chemotion-converter-app/releases/tag/v1.1.1

    Refs: #1634

commit 1e43e364e7c4a4d79ac6b3ce0231ccb1890ca13f
Author: TasnimMehzabin <[email protected]>
Date:   Fri Nov 17 12:33:07 2023 +0100

    fix: the attachment to be removed from the inbox when assigned to a sample (#1631)

    Co-authored-by: Tasnim Mehzabin <[email protected]>

commit a31a0ffdf84c81e6674b942f4272410431876073
Author: Adam Basha <[email protected]>
Date:   Thu Nov 16 08:54:43 2023 +0100

    feat: include chemicals with import and export of collections (#1604)

commit d6c6c9609544343e3d326c086d9c4078567a3778
Author: Pei Chi Huang <[email protected]>
Date:   Thu Nov 16 06:41:31 2023 +0100

    feat: drag samples and elements to segment (#1623)

commit c1e26a2fb8970fbf3ac54c1e40170e98f89effe2
Author: PiTrem <[email protected]>
Date:   Thu Nov 16 06:40:34 2023 +0100

    feat: display mail collector address as info in the Inbox (#1529)

    send mail collector address to client if mail collector is configured

    (the last registered alias over the ui api)

    add info button for collecting file per email in inbox modal

    click to copy collector address  to clipboard

    ---------

    Co-authored-by: nh9378 <[email protected]>

commit 09ec1599c0a17ec153b0fdc3941178f85c79a7ee
Author: Lan Le <[email protected]>
Date:   Tue Nov 14 12:29:32 2023 +0100

    feat(spectra): update chemspectra backend to read some jcamp v6 (#1603)

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

commit 8203debbcfa84f7efb7d06021da63421b03e737a
Author: f-idiris <[email protected]>
Date:   Tue Nov 14 12:28:20 2023 +0100

    feat: report peaks from XRD (#1614)

commit da0074b4e3a585baf37698f8e6015cf624de7091
Author: Pei Chi Huang <[email protected]>
Date:   Tue Nov 7 12:30:53 2023 +0100

    feat: better grouping of decoupled samples in list (#1612)

commit ab9f67a5c4ea265edcf5ae7396a160676d067fdc
Author: Lan Le <[email protected]>
Date:   Mon Nov 6 17:36:08 2023 +0100

    fix: polymer bead not visible in reaction svg

    update react-svg-file-zoom-pan to version 1.1.2 so that the polymer bead representation is visible on the reaction preview and detail images.

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

    refs: #1607

commit be8e927e95f7f7383638e688ed3fa4e742a19986
Author: TasnimMehzabin <[email protected]>
Date:   Thu Nov 2 10:15:17 2023 +0100

    feat: add the option to sort reaction list by updated time (#1461)

    * feat: add the option to toggle reaction sort direction

    * fix: update the filter message in the elements table list

    ---------

    Co-authored-by: Tasnim Mehzabin <[email protected]>

commit c61c86a162270ff0c3a2ac5d4806d23ed40bed18
Author: TasnimMehzabin <[email protected]>
Date:   Fri Oct 27 10:51:03 2023 +0200

    feat(UI): file size is listed in the analyses tab

    Refs:  #1601
    Co-authored-by: Tasnim Mehzabin <[email protected]>

commit 6f1afba3a0861363e18962df96128d478647989a
Author: TasnimMehzabin <[email protected]>
Date:   Thu Oct 26 13:34:19 2023 +0200

    feat(UI): remove redundant inbox section from the collection listing on the left panel

    - leave the left panel for collection browsing
    - Inbox is now only, but clearly, called from the top menu bar

    Refs: #1593

    Co-authored-by: Tasnim Mehzabin <[email protected]>

commit 84c02bced038ef307abb67393a86a3fe71f8bb35
Author: Pei Chi Huang <[email protected]>
Date:   Wed Oct 25 09:48:20 2023 +0200

    feat: converter trigger on attachment inbox items

    Refs: #1583

commit 75fde46a36618f7c887408ff11628bf865a5150f
Author: PiTrem <[email protected]>
Date:   Tue Oct 24 22:20:11 2023 +0200

    chore: update VERSION 1.8.0

    chore: update ci image

    chore: minor node upd

    chore: upd changelog

    chore: .gitignore do not track doc/

    Refs: #1576

commit 7bd6a5d811aa6cce2d702418fa502dc3e90f9509
Author: Pei Chi Huang <[email protected]>
Date:   Tue Oct 24 11:52:45 2023 +0200

    fix(UI): reaction list display break when reaction status not standard

    Rendering of Overlay component break UI when a reaction status goes to the switch default case.

    For example on shared reaction with limited permission (reaction.status = "***")

    Refs: #1592

commit 2659436039ac49e87720a09833efdeb330c60c9b
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Oct 24 10:53:22 2023 +0200

    chore: Bump @babel/traverse from 7.16.10 to 7.23.2 (#1580)

    Bumps [@babel/traverse](https://github.com/babel/babel/tree/HEAD/packages/babel-traverse) from 7.16.10 to 7.23.2.
    - [Release notes](https://github.com/babel/babel/releases)
    - [Changelog](https://github.com/babel/babel/blob/main/CHANGELOG.md)
    - [Commits](https://github.com/babel/babel/commits/v7.23.2/packages/babel-traverse)

    ---
    updated-dependencies:
    - dependency-name: "@babel/traverse"
      dependency-type: indirect
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit 48aef3b04ae3aca429755d4da6f9550237f12e00
Author: Pei Chi Huang <[email protected]>
Date:   Tue Oct 24 10:46:19 2023 +0200

    feat: expand calendar function to generic element

    Refs: #1585

commit 3ef1129914dfb73b32d54b1a52cbd7b65009d7e7
Author: Adam Basha <[email protected]>
Date:   Tue Oct 24 06:58:59 2023 +0200

    fix: reaction calculation when no reference material present

    fix break introduced with 40bc206fb0

    Ref: #1589

commit 5f6d6ad50a698903825fa398f842286020dd78eb
Author: Pei Chi Huang <[email protected]>
Date:   Mon Oct 16 09:27:08 2023 +0200

    chore: update labimotion - converter ui  (#1578)

    fix: converter app call not triggered

commit 6b1438478040eb356be4dcc80152d3c7b3f965a4
Author: Lan Le <[email protected]>
Date:   Tue Oct 10 10:11:06 2023 +0200

    fix: hide spectra button when only uploading an image (#1568)

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

commit 10ef1f11cd39750ccdb72df4152dfedf6af56c44
Author: Adam Basha <[email protected]>
Date:   Tue Oct 10 10:10:05 2023 +0200

    fix: assign only boolean values for decoupled column when importing samples (#1571)

commit 894306a126f6f1546825235eee256dc51ffd8316
Author: PiTrem <[email protected]>
Date:   Tue Oct 10 08:49:55 2023 +0200

    fix: Admin seed: ensure exisiting Admins have a profile (#1572)

    - fix: navigation/call to user-profile depending page/action

    - fix: README links to docs (trailing '/' routing)

commit e2ee14b1d824a03a203920947965da8498980e4b
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Tue Oct 10 08:48:02 2023 +0200

    chore: Bump @adobe/css-tools from 4.2.0 to 4.3.1 (#1511)

    Bumps [@adobe/css-tools](https://github.com/adobe/css-tools) from 4.2.0 to 4.3.1.
    - [Changelog](https://github.com/adobe/css-tools/blob/main/History.md)
    - [Commits](https://github.com/adobe/css-tools/commits)

    ---
    updated-dependencies:
    - dependency-name: "@adobe/css-tools"
      dependency-type: indirect
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit 3de16fa33e1bdb7eaba46c3f793fd346aca7ac83
Author: PiTrem <[email protected]>
Date:   Mon Oct 9 16:08:16 2023 +0200

    fix:  rollback labi version up (#1570)

commit 0781e5cda2d2b25a430193018ea5cf46d22799e3
Author: PiTrem <[email protected]>
Date:   Mon Oct 9 13:59:49 2023 +0200

    prep v1.8.0-rc2

commit c4200dffad7d30f20aa0b7cb1654ba21cc11c63b
Author: PiTrem <[email protected]>
Date:   Mon Oct 9 13:53:52 2023 +0200

    chore: minor dep updates (#1569)

    * chore: minor update sentry

    * fix: typo env var for sentry monitoring

    * chore: update service dep

    * fix: downgrade labimotion to prevent converter process early exit

    * chore: yarn audit fix

commit d55520d512d40502b455b54d39c912ef54c0facb
Author: Lan Le <[email protected]>
Date:   Mon Oct 9 13:48:18 2023 +0200

    feat: update chemspectra to change value of referent solvent (#1557)

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

commit bebdec0eea8170f21a36e97f64756b0aaf84a279
Author: Mostafa Mekky <[email protected]>
Date:   Mon Oct 9 13:05:19 2023 +0200

    fix: sample properties tab (#1503)

    * Fix: style issue for boxes in sample

    * Enhancement: hide labels when there is no solvent

    * Decoupled checkbox padding

    * test: add test for SampleSolvent rendering

    * test: add test for SolventDetails rendering

    ---------

    Co-authored-by: FabianMauz <[email protected]>

commit be0bcd83da967882e3e912f2d9ed58ccf302caf6
Author: Lan Le <[email protected]>
Date:   Mon Oct 9 12:45:08 2023 +0200

    feat: show nmrium button for reaction and research plan (#1471)

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

commit ee881fefd4ce37da533db58a325687c0320e71fa
Author: Jan C. Brammer <[email protected]>
Date:   Mon Oct 9 12:35:31 2023 +0200

    feat: update reaction variations (#1567)

    * Rename variable for consistency

    * Use React Bootstrap buttons

    * Identify variations with sequential ID

    * Add vertical space around table tools

    * Remove uncessary guard

commit 3c0b1e4de6af5a3870ce6c4f6eac2947749cbf40
Author: Fabian Mauz <[email protected]>
Date:   Fri Oct 6 10:53:09 2023 +0200

    fix: no attachments after research plan save

    * fix: add Attachment Fetcher as uploader for attachments

    * fix: upload attachments via AttachmentFetcher

    * fix: add needed parameter for next promise step

    * fix: upload attachments in genericElsFetcher only if no researchplan

    * fix: create multiple attachments on researchplan create

    * test: add tests for getting attachments of researchplan

    * fix: removed deprecated thumbnail job

    * fix: WIP map identifier to attachment

    * fix: removed index from loop

    * fix: add identifier to params

    * refactor: use loop with index instead of own index variable

    * todo: remove uploading of attachments via GenericElsFetcher and do the same for update usecase

    Refs: #1564
    ---------
    Co-authored-by: nh9378 <[email protected]>

commit c1b45ae4105d2d19e74b88a5761cb41eb873e128
Author: Adam Basha <[email protected]>
Date:   Thu Oct 5 19:07:28 2023 +0200

    feat: Import export sample as chemical

    * implementation for import chemicals to collection, added import_chemicals class and spec tests and refactored import_samples class to add import_type option to import samples

    * refactor construct_p_statements and construct_h_statements methods in chemical_service to solve duplication issue and refactored chemicals_service_spec tests accordingly

    * handle failing of import chemicals (sample will not be created, user will be notified which samples could not be imported, refactor import_chemicals and spec tests

    * allow import cas field on sample import for xlsx format

    * import chemicals: allow skipping import of chemical field if column header is null

    * refactor report_api code for exporting samples and chemicals

    * refactor code of export chemicals in report_helpers module into own class and improve export functionality of chemicals

    * write unit tests for ExportChemicals class

    * disable sdf format option for chemicals export and adjust exportModal height

    * refactor ExportImportButton component

    * refactor report_helpers module and import_samples_spec  to fix failing spec in report_api_spec and import_samples_spec

    * allow import of decoupled samples

    * allow import & export of decoupled samples

    * allow SDS search for chemical when molecule does not exist (for decoupled samples)

    * allow import of merck safety sheets on import chemicals

    * allow import of float amount values for import chemicals

    * allow sample import with case insensitive values of decoupled column

    Refs: #1524

commit 77a091b7689af3731ae356791794cfc081eac3f4
Author: Lan Le <[email protected]>
Date:   Thu Oct 5 19:02:52 2023 +0200

    fix: add filter for NMR kind

    check if NMR CHMO entry is an ancestor
    Co-authored-by: Lan Le <[email protected]>
    Ref: #1563

commit 10d35642ccb7e11b448fd6f06164171bf75b2d7f
Author: TasnimMehzabin <[email protected]>
Date:   Thu Oct 5 08:40:55 2023 +0200

    feat: add a checkbox for dry solvents in the solvents section in the reactions table

    * add a checkbox for dry solvents in the solvents section in the reactions table
    add option to mark sample as dry solvent

    * refactor the code to fix rubocop warnings

    * allow import of dry_solvent attribute in import samples for xlsx and sdf formats

    * adjust dry-solvent element width in sampleForm component

    Refs:  #1432
    ---------

    Co-authored-by: nh9378 <[email protected]>

commit 1795b4b0729e0aea14909438099db628baf20c9c
Author: Adam Basha <[email protected]>
Date:   Thu Oct 5 08:36:14 2023 +0200

    fix: load cas for molecules

    * fix loading cas when using pubchem service

    Refs: #1555

commit 1211fd6b0694e4485af951742b5aba037a296916
Author: TasnimMehzabin <[email protected]>
Date:   Thu Oct 5 07:55:25 2023 +0200

    fix: current_user.matrix getting null value

    Refs: #1554

commit c5c7b2faf4c7161d6e52dc4bd75ea976e1f54e4f
Author: Adam Basha <[email protected]>
Date:   Thu Oct 5 07:54:43 2023 +0200

    fix: show example reaction label in settings page

    Refs: #1556

commit 06aa179b1fea53dc393cfc93877c69369e369509
Author: Jan C. Brammer <[email protected]>
Date:   Thu Oct 5 07:52:47 2023 +0200

    feat: update reaction variations

    * Use `name` as default material identifier

    * Allow zero ('0') values

    * Extend tooltip

    * Make inclusion of `variations` in report optional

    * Guard against missing material types

    * Allow any precision for numerical input

    Refs #1561

commit e73d76ed36e5ba214d9033c709b0d25fa210c7f6
Author: TasnimMehzabin <[email protected]>
Date:   Wed Sep 27 15:56:52 2023 +0200

    fix: comment fetch issue on new entities

    Refs: #1547

commit 9992a85878d4fb272b4fca9639b8d35f3c93f3f6
Author: Lan Le <[email protected]>
Date:   Wed Sep 27 15:54:56 2023 +0200

    chore: update chemspectra backend version to display label cv layout

    Co-authored-by: Lan Le <[email protected]>
    Refs: #1546

commit ba6c1d9af0334da5a86c23d14e64714e0fe3a7f7
Author: Lan Le <[email protected]>
Date:   Wed Sep 27 09:36:41 2023 +0200

    feat: display combined image as preview if it exists

    fixed: fix UI issue on CV layout

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

    Refs: #1526

commit 1a9fc9e730f24ffed42ef928b3938693a47e47ff
Author: PiTrem <[email protected]>
Date:   Fri Sep 22 13:23:25 2023 +0200

    fix: wrong conflict resolution (#1542)

commit fc4bf31e40400f43c88604a36396b886f6ef073e
Author: PiTrem <[email protected]>
Date:   Fri Sep 22 09:00:35 2023 +0200

    test: update runner image (#1541)

commit 154e18cea48ddd3b4c1c7b45623d16d501ca59a9
Author: Mostafa Mekky <[email protected]>
Date:   Thu Sep 21 15:06:56 2023 +0200

    test: "yarn test" errors & warnings

    * fix: removed useless prop "bsSize"

    * fix: added polyfills for unsupported browsers

    * fix: used instance of attachement

    * fix: disabled lifecycle update for testing

    * fix: added attachments as prop

    * Refactor: stub ChemicalFetcher.create & eslint fix

    * Fix: yarn test errors for ChemicalTab

    Refs: #1523

commit 4bd661989e4e1d98f8b0fee733794f0e20197299
Author: PiTrem <[email protected]>
Date:   Wed Sep 20 07:19:47 2023 +0200

    chore: prep v1.8.0-rc1

commit 98665123f0ab527ee71537eef2e0b3c43c9d1d69
Author: Pei Chi Huang <[email protected]>
Date:   Wed Sep 20 07:12:07 2023 +0200

    feat: LabiIMotion Integration

    * Generic Element
    * Generic Segment
    * Generic Dataset

    Refs: #1504

    ---------

    Co-authored-by: Claire Lin <[email protected]>

commit 728e95ff4388fd9cb34e2bd6b582e1fd341e952b
Author: PiTrem <[email protected]>
Date:   Wed Sep 20 07:04:50 2023 +0200

    fix: assets precompilation css issue

    ```
    SassC::SyntaxError: Error: "var(--ag-internal-calculated-line-height)" is not a number for `min'
            on line 2381:11 of stdin, in function `min`
            from line 2381:11 of stdin
    >>   height: min(var(--ag-internal-calculated-line-height), var(--ag-internal-p
    ```
    Refs:  #1538

commit 1b540e188ca8da89f71a4bcecd9b70cb0e65099f
Author: Jan C. Brammer <[email protected]>
Date:   Wed Sep 20 07:01:01 2023 +0200

    feat: Reaction Variations

    * Add variations tab to reaction detail modal

    * Update `ag-grid` JS dependencies

    * Correctly deconstruct `material.amount`

    * Try using material labels as column headers

    * Extend example data structure for clarity

    * Show cell entries with three decimal places

    * Individualize reference material per row

    Make reference material immutable

    * Add auxiliary properties to variation materials

    * Compute yield

    * Update style

    * Update variations object on edits

    * Auto-size columns with min width

    * Add tooltip

    * Fix initialization of variations

    * Move variations-related logic into utils

    * Rename `utils` to `ReactionVariationsUtils`

    * Add tests for reaction variations

    * Remove toggeable material groups

    * Make unit selection more explicit

    * Don't cache reaction

    * Write reaction variations to .docx report

    * Consistently set product unit to `Amount`

    * Properly anonymize variations

    * Don't compute yield if `referenceMaterial` is missing

    * Remove redundant entry from entity definitions

    * Add `ReactionVariationEntity`

    * Use sub-entity for material aux

    * Make RuboCop happy

    * Make rows sortable by columns

    * Make rows draggable

    * Add row ID to tool-column

    * Make columns resizable

    * Prevent sub-columns from separating on dragging

    * Increase number of decimal places

    * Make material identifier configurable

    * Factor out `convertTemperature`

    * Make units configurable

    * Add column for solvents

    * Refactor: parametrize material types

    * Enforce specific units per material type

    * Add editable equivalents

    * Add molar mass to hover-over

    * Revert unused export

    Refs: #1409

commit 27b7dcde95de5d6af6e31e038243950bbbc78822
Author: Mostafa Mekky <[email protected]>
Date:   Wed Sep 20 06:59:25 2023 +0200

    Feat: filter options for admin user management

    * Eslint fixes

    * Feat: filter options for admin user management

    Refs: #1510

commit 0c39f7b4e7585c2058047f047ebc73a69487c441
Author: Johannes Haubold <[email protected]>
Date:   Wed Sep 20 06:54:49 2023 +0200

    feat: Move sample task inbox to header bar

    Refs: #1517

commit dc4283bbd6c15d12fd27fc42f157eb465e29d882
Author: Adam Basha <[email protected]>
Date:   Wed Sep 20 06:54:03 2023 +0200

    feat: Enhance import samples for sdf

    * refactor export of sample solvent to export solvent name(not the solvent hash)- refactor export samples for sdf for melting and boiling points columns and write import sample job for sdf format and refactor and write  import samples jobs spec tests for sdf format

    * fix typo & refactor boiling and melting points params in sample_api_spec test

    * add density column to import samples with sdf format and refactor sample_api_spec file

    * improve extract solvent and other functions for sdf export

    Ref: #1364

commit fc4d28661c4b4b4550fea71543dee1d9b1e73bf7
Author: PiTrem <[email protected]>
Date:   Wed Sep 20 06:48:58 2023 +0200

    chore: prep v1.7.3 (#1537)

commit ff9b54715e5a7620609593996dff6a56eaf2ea02
Author: PiTrem <[email protected]>
Date:   Tue Sep 19 12:57:43 2023 +0200

    feat: update ext links in the Navbar menu dropdown

    - update links (added docu, removed kit/complat)

    - DRY

    - also added external-link icon to make clear the link is leaving the current domain.

    Refs: #1534

commit 605cea9750f031f2864d2e78ddd268d5b2f37181
Author: PiTrem <[email protected]>
Date:   Tue Sep 19 09:12:22 2023 +0200

    fix: reaction sort column default to created_at (#1533)

    After updating (from1.7.2 to efecaf8a9c), the user profile does not have yet filter.reaction.

    The default reaction sorting in the UI is 'list' (should be `created_at` descending)

    but the client will sent sort_column=updated_at instead of created_at thus confusing the user.

    thorough resolution should come with PR #1461

commit 38445b80af45de3df2f0b76c32c660a17f68ffe9
Author: Jan C. Brammer <[email protected]>
Date:   Mon Sep 18 14:52:43 2023 +0200

    chore: Add Cypress dependencies to Dockerfiles

    * Add Cypress dependencies to CI Dockerfile

    * Add Cypress dependencies to Dev Dockerfile

    Refs: #1491

commit f3e010eaf23e0074803f6379c04ea1055741af12
Author: Johannes Haubold <[email protected]>
Date:   Mon Sep 18 14:48:33 2023 +0200

    feat: Show sample name in SampleTask Api

    * Show sample name in SampleTask Api

    * Fix rubocop issue

    * Fix spec

    Refs: #1518
    ---------

    Co-authored-by: Matthias Döring <[email protected]>

commit 40bc206fb0aeff7c6aad6bdec75259af53fad571
Author: Adam Basha <[email protected]>
Date:   Mon Sep 18 12:01:33 2023 +0200

    fix: yield percentage error for reactions with decoupled products and disable error message for decoupled samples

    Refs: #1531

commit d97121d94538a4357e53f2308f56e51c18ed5e41
Author: f-idiris <[email protected]>
Date:   Fri Sep 15 16:33:58 2023 +0200

    feat: Add select all option for device inbox folder

    * 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

commit 823c5116c0a3a1c566a775946a9f8acfae1eb1b7
Author: Lan Le <[email protected]>
Date:   Fri Sep 15 16:30:04 2023 +0200

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

    fix:  cannot read processed data from Bruker

    Co-authored-by: Lan Le <[email protected]>
    Refs: #1528

commit 74215ebd0dceac135e845933c5dfc53021e35e30
Author: Lan Le <[email protected]>
Date:   Fri Sep 1 12:00:45 2023 +0200

    fix: check the nmrium file before ignore generate

commit d8ba70f0743cfe99bbaba2591ed9fbbb4e47947e
Author: Lan Le <[email protected]>
Date:   Mon Aug 28 14:37:19 2023 +0200

    feat: update chemspectra frontend to fix bugs

commit 03b28ce207b5de6e29582550efc0d5467ba9bf0a
Author: Lan Le <[email protected]>
Date:   Fri Aug 25 13:16:47 2023 +0200

    fix: ignore predictions when it is null

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

    Refs: #1507

commit 81ad5d081112111bd38f72ac0042bb0fa7ba80be
Author: Fabian Mauz <[email protected]>
Date:   Fri Aug 25 12:34:10 2023 +0200

    fix: fixed wrong literatures mapping

    Refs: #1506

commit e29301f949fba54748b70116b0016b698cc0f60b
Author: Fabian Mauz <[email protected]>
Date:   Fri Aug 25 10:46:35 2023 +0200

    fix: patch citationjs to process doi-sici

    * 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

commit 54871a323cbad54d0d5557f1f9beac5550365387
Author: PiTrem <[email protected]>
Date:   Fri Aug 25 10:45:02 2023 +0200

    chore: upg nodejs LTS to 18

    * 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

commit 37acd1675050e0b76b4e0bd3e738e8dd224f1c5f
Author: Fabian Mauz <[email protected]>
Date:   Fri Aug 25 10:32:17 2023 +0200

    fix: deletion of literature

    * 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

commit 24bf00c515fc85678b85555d4ea215bb01c80ee7
Author: TasnimMehzabin <[email protected]>
Date:   Thu Aug 24 11:28:05 2023 +0200

    feat: add more reagent to the reaction table reagent dropdown

    * 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

commit 4aa09febbd9bd7d056b4b6f254c1c11b2d7429f2
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Thu Aug 24 10:23:38 2023 +0200

    chore: Bump puma from 5.6.5 to 5.6.7

    Bumps [puma](https://github.com/puma/puma) from 5.6.5 to 5.6.7.
    - [Release notes](https://github.com/puma/puma/releases)
    - [Changelog](https://github.com/puma/puma/blob/master/History.md)
    - [Commits](https://github.com/puma/puma/compare/v5.6.5...v5.6.7)

    ---
    updated-dependencies:
    - dependency-name: puma
      dependency-type: direct:production
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

    Refs: #1488

commit 4e781496197cc604800b4470fcff3b872902e13e
Author: TasnimMehzabin <[email protected]>
Date:   Thu Aug 24 08:54:04 2023 +0200

    fix: inbox UnsortedBox issues

    * fix: inbox UnsortedBox issues

    * fix the issue with attachment deletion in UnsortedBox.js
    * fix the UnsortedBox section closing on file upload

    * fix: add draggable cursor icon for the inbox header

    Refs:  #1447

commit b812b48f098f2c0c64f945087a88d6645589c2d6
Author: Lan Le <[email protected]>
Date:   Thu Aug 24 08:52:12 2023 +0200

    fix(spectra): sorting multiplicity values

    Co-authored-by: Lan Le <[email protected]>
    Refs:  #1478

commit 9ea494f22a6602692cd3dfae6fd59a0634e6bdc4
Author: f-idiris <[email protected]>
Date:   Thu Aug 24 08:51:11 2023 +0200

    fix(spectra): prevent regenerating spectrum and duplicating jdx

    fix: fix duplicated png peak file

    Refs: #1479

commit 79cc12b50f8b7afc14046c6e6fe4a73b2426cfe0
Author: Johannes Haubold <[email protected]>
Date:   Tue Aug 22 10:36:44 2023 +0200

    fix: replace toSorted with manual sorting in SampleTaskInbox

    Refs: #1485

commit 5d2cf58096137571fe83c81ff247952f89b7f790
Author: Lan Le <[email protected]>
Date:   Fri Aug 18 09:53:10 2023 +0200

    feat: update version of chemspectra

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

    Refs: #1480

commit 0735f723302fb5cd12cb43abafad581a91e631ae
Author: Lan Le <[email protected]>
Date:   Fri Aug 18 09:51:13 2023 +0200

    chore: update information of chem-spectra-app

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

    Refs:  #1484

commit f75d55439f856b4f7e2dfffee3d2fbf2f2bcd4f6
Author: Lan Le <[email protected]>
Date:   Thu Aug 17 15:57:35 2023 +0200

    fix: hide NMRium button on non-NMR layouts

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

    Refs: #1460

commit aa30d087c328af7d210074bd671fd3b0c9375892
Author: Lan Le <[email protected]>
Date:   Wed Aug 16 14:52:48 2023 +0200

    fix: 2D to work with new nmrium wrapper version

    feat: update function to save content for layout 15N, 29Si and 31P

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

    Refs: #1436

commit 8347fe8e145aa56773725e78626693bd5a727329
Author: Mehmood Ghaffar <[email protected]>
Date:   Wed Aug 16 13:19:20 2023 +0200

    Fixed Cypress Tests (#1481)

    * create user test  and researchplan extended test are added

    * collections api spec is now added

    * deleted unnecessary comments from collection_api_spec.cy.js

    * Remove redundant API test for now (conceptually replicated RSpec)

    * fixed failing test cases due to changes in chemotion ELN

    * fixed failing test and removed typos

    ---------

    Co-authored-by: Jan C. Brammer <[email protected]>

commit 412899294a67832fcbb6fba8179adb78fa770695
Author: PiTrem <[email protected]>
Date:   Tue Aug 15 10:11:35 2023 +0200

    chore: update README - acknowledge NFDI4Chem

    Refs: (#1472)

commit 98a50308a03e80d6716dedebdf7c38d25f6b9092
Author: Mostafa Mekky <[email protected]>
Date:   Tue Aug 15 09:47:54 2023 +0200

    style: wellplates multiple readouts design tab

    * fix: popover out of bounds

    Refs: #1474

commit 953a2057a17aabad5e6f2d8ed6bd6e7cbc589c3a
Author: Mostafa Mekky <[email protected]>
Date:   Tue Aug 15 09:46:55 2023 +0200

    fix: white screen research plan

    ✅  style: better toggle
    ✅  style: better & consistent  name-link in the reaction/sample image
    ✅  fix:  showDetails issue when opening from list

    Ref: #1452

commit 6816ee1293117a162a4256941384dca9b13d5dcd
Author: Lan Le <[email protected]>
Date:   Thu Aug 10 16:08:32 2023 +0200

    feat: add Emission, DLS ACF, DLS intensity layouts

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

    Refs: #1374

commit 9ca632a4ebfe8e7a22358812880dbd94d4dbe3cc
Author: Mostafa Mekky <[email protected]>
Date:   Thu Aug 10 13:40:11 2023 +0200

    style: add-analysis button always visible

    Refs:  #1465

commit ecf57bea92255ed39b190afb8f6a830aa93c3b4c
Author: Fabian Mauz <[email protected]>
Date:   Thu Aug 10 13:28:32 2023 +0200

    fix(UI): image annotation tool image preview - force rerendering

    * fix: force rerendering after attachment preview change

    After changing/adding an attachment the preview variable of all attachments are reloaded, but the "refreshed" attachments are not set to the react state. I will force now a rerendering after the reload of the preview

    * style: eslint autofixes + method order fixes + react/destruct

    * test: add test for checking correct rendering

    Refs: #1467

commit a1c2d5b295a2438b046a129c8562fcf8e19116ce
Author: PiTrem <[email protected]>
Date:   Thu Aug 10 13:19:11 2023 +0200

    fix: display not-accessible info for 401 status on sample fetched by id

    * fix navigation to existing sample without permission:
    when a query to fetch sample by id returns 401, the not accessible panel should be rendered

    * now also render the info panel for record (sample/reaction) not found (404)

    Ref: #1469

commit 10eb0d00be6d16ddb80ac95dbe5b5eae4f4e46a2
Author: PiTrem <[email protected]>
Date:   Wed Aug 9 13:30:16 2023 +0200

    fix: quill_to_html when type HashWithIndifferentAccess

    * also refactor: schmooze implementation

    Refs: #1458

commit cdab7e71fa0cc2e2369a2f04a3619f1d79546256
Author: Johannes Haubold <[email protected]>
Date:   Wed Aug 9 13:29:33 2023 +0200

    Always sort new sample tasks on top of list (#1456)

commit ce8cab87f435c82b86468ff88c57d73d3b821a01
Author: Pei Chi Huang <[email protected]>
Date:   Thu Aug 3 16:59:45 2023 +0200

    chore: disable chem repository id fetch job

    as the resource is being updated

commit 4d0c913c2dd6512acfaefa1ab34f3f8c4bfd2633
Author: Pei Chi Huang <[email protected]>
Date:   Wed Aug 2 15:29:24 2023 +0200

    chore: upgrade convert 1.0.0

    Refs: #1450

commit 2467be7906c759a3ab136109edcd9bb44e3e4ff6
Author: Johannes Haubold <[email protected]>
Date:   Tue Aug 1 16:02:27 2023 +0200

    feat: Allow deletion of SampleTasks and fix SampleTask Inbox scroll issues

    * Allow deletion of SampleTasks and fix SampleTask Inbox scroll issues

    * Add confirmation dialog when deleting a sample task

    * Improve deletion dialogue

    * Add spec for DELETE sample task endpoint

    * Rubocop

    Refs:  #1444

commit 1515f963644e65dd5b16985d09007b695df7c358
Author: PiTrem <[email protected]>
Date:   Tue Aug 1 13:20:41 2023 +0200

    fix(UI): missing generic element icon

commit f6148e650c66c21b7d3d7acf86cc5391000106cf
Author: PiTrem <[email protected]>
Date:   Tue Aug 1 12:06:44 2023 +0200

    chore: prepare v1.7.2

commit 2d8e2fabd621dcc0a00e3d0c5291a770c070006f
Author: TasnimMehzabin <[email protected]>
Date:   Mon Jul 31 15:56:23 2023 +0200

    fix: Comment functionality

    * fix the CSS for header comment buttons to keep them together on smaller screens
    fix the display of the comment count in the reactions' list

    * refactor the code to fix linting warnings

    * refactor the code show the action of the products only toggle button

    * add comment section for the inventory tab in samples

    Ref:  #1435

commit 4922fc39488a97afcc2b4466ae6cbf02a6776ba2
Author: TasnimMehzabin <[email protected]>
Date:   Mon Jul 31 15:53:47 2023 +0200

    fix: Sort reactions by creation time

    * fix the sort query based on the action stated in the sort icon for reactions

    Refs: #1439

commit e08d8cd1186763c090539b191f237cd5367b1016
Author: Lan Le <[email protected]>
Date:   Mon Jul 31 15:48:11 2023 +0200

    fix display wrong shifted peaks after zoom (#1443)

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

commit cd4048efb5341a5362b98d41538f4509db1092a1
Author: PiTrem <[email protected]>
Date:   Wed Jul 26 11:57:18 2023 +0200

    chores: VERSION

commit 05acee669233a93dc63b897af2e350a02dcd2f90
Author: PiTrem <[email protected]>
Date:   Fri Jul 21 15:26:58 2023 +0200

    chores: clean stylesheet from plugin integration remnant

commit cd9b7132d1d28b862a6da3dbba434f5c18a376a0
Author: Mehreen Mansur <[email protected]>
Date:   Wed Jul 26 11:50:41 2023 +0200

    fix(UI): available tab options

    * - include tab option from profile data
    - filter null values in hidden tab list

    Refs: #1427

    ---------

    Co-authored-by: Mehreen <mehreen.mansur>
    Co-authored-by: PiTrem <[email protected]>

commit 3cae2fdd95153dfe91ed9d6ed40a82a9456191a1
Author: Mehreen Mansur <[email protected]>
Date:   Wed Jul 26 11:20:49 2023 +0200

    style: add edit icon in collection tabs

    Refs: #1425
    Co-authored-by: Mehreen <mehreen.mansur>

commit efecaf8a9c1d5b68ba23eca2e75eb0c8a177ef5c
Author: TasnimMehzabin <[email protected]>
Date:   Wed Jul 26 10:41:58 2023 +0200

    fix: sort reaction list by created_at

    * modify the reaction list sorting to default to created_at as in < v1.7.0
    disable the sort toggle for reaction list
    modify the sort icon popup text
    modify the test codes as reaction list is sorted by created_at by default

    Ref: #1429

commit 7d4dd22d8a246e1e0c0f680d0af832464305b368
Author: Lan Le <[email protected]>
Date:   Wed Jul 26 10:26:29 2023 +0200

    fix(chemspectra): cannot change ref area and display wrong shift

     Refs: #1431

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

commit baa6a4fa9f15068115465fb9e2b4d203f294b865
Author: Mehreen Mansur <[email protected]>
Date:   Mon Jul 24 08:58:46 2023 +0200

    fix: total element count in list-tabs (#1426)

    Co-authored-by: Mehreen <mehreen.mansur>

commit 7fe6e5834a484cbb8c70995fdbcf32d492864700
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Jul 21 13:21:59 2023 +0200

    Bump word-wrap from 1.2.3 to 1.2.4 (#1421)

    Bumps [word-wrap](https://github.com/jonschlinkert/word-wrap) from 1.2.3 to 1.2.4.
    - [Release notes](https://github.com/jonschlinkert/word-wrap/releases)
    - [Commits](https://github.com/jonschlinkert/word-wrap/compare/1.2.3...1.2.4)

    ---
    updated-dependencies:
    - dependency-name: word-wrap
      dependency-type: indirect
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit 313f34222c836a2eff72623653b14e49eae0d872
Author: TasnimMehzabin <[email protected]>
Date:   Fri Jul 21 13:14:16 2023 +0200

    featfix: Add the option to sort reactions based on short_label or updated_at

    * add the option to sort reactions based on short_label or updated_at

    * modify the test cases since default reaction sorting is based on short_label in place of updated_at

    * fix the sort query based on the action stated in the sort icon for reactions
    implement short_label descending sort for reactions
    modify sort icon texts
    modify the test cases as short_label desc sort is applied

    * modify the sort icon to display the current sort state
    modify the pop over text of the sort icon to describe the sorting action on click and also the current sort state

    Refs: #1418

commit 97fe249a05857131e7ff31b7010e1470f7a68b01
Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Date:   Fri Jul 21 12:56:24 2023 +0200

    Bump semver from 5.7.1 to 5.7.2 (#1403)

    Bumps [semver](https://github.com/npm/node-semver) from 5.7.1 to 5.7.2.
    - [Release notes](https://github.com/npm/node-semver/releases)
    - [Changelog](https://github.com/npm/node-semver/blob/v5.7.2/CHANGELOG.md)
    - [Commits](https://github.com/npm/node-semver/compare/v5.7.1...v5.7.2)

    ---
    updated-dependencies:
    - dependency-name: semver
      dependency-type: indirect
    ...

    Signed-off-by: dependabot[bot] <[email protected]>
    Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

commit ee68158d7973acfc5b8deedf2c41ce0715ff7fb7
Author: TasnimMehzabin <[email protected]>
Date:   Thu Jul 20 14:01:44 2023 +0200

    Refactor the private note api (#1414)

    * refactor the private_note_api.rb
    refactor the PrivateNoteFetcher.js
    refactor the private_note_api.spec.rb

    * fix rubocop warning

commit ee2db103777d443dd490c51da9a7b8933a561eb5
Author: f-idiris <[email protected]>
Date:   Tue Jul 18 12:54:57 2023 +0200

    Fix inbox (de)select boxes (#1416)

    * fix checkbox for `unsorted` list

    * select/deselect/delete for current page only

    * update renderCheckAll

commit 3645d848bf9eb3b3c8347d9b61b543cf94071d2a
Author: f-idiris <[email protected]>
Date:   Mon Jul 17 09:42:35 2023 +0200

    fetch attachment preview for new attachments only (#1410)

commit b82e7222cf47460a92a08e547035d3e128bcb3f7
Author: Mehreen Mansur <[email protected]>
Date:   Fri Jul 14 16:20:55 2023 +0200

    Sync collection tab segments fix (#1411)

    * - tabs segment for sync collection entity
    - add css for tab cell

    sync collec entity to return empty tab_segment profile

    remove tab_segments from sync_collec_user entity

    * extract string utility function

    ---------

    Co-authored-by: Mehreen <mehreen.mansur>
    Co-authored-by: PiTrem <[email protected]>

commit 77f83bfd132101bd69efec380923f9ad47e7aa94
Author: Adam Basha <[email protected]>
Date:   Fri Jul 14 15:40:26 2023 +0200

    fix bug undefined current_user for collectionEntity on reaction docx … (#1412)

    * fix bug undefined current_user for collection…
baolanlequang pushed a commit that referenced this pull request Mar 5, 2024
@adambasha0
feat: Enhance import samples for sdf
714edae 
* refactor export of sample solvent to export solvent name(not the solvent hash)- refactor export samples for sdf for melting and boiling points columns and write import sample job for sdf format and refactor and write  import samples jobs spec tests for sdf format

* fix typo & refactor boiling and melting points params in sample_api_spec test

* add density column to import samples with sdf format and refactor sample_api_spec file

* improve extract solvent and other functions for sdf export

Ref: #1364
@PiTrem PiTrem deleted the enhance_import_samples_for_sdf branch June 14, 2024 19:19
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