fix wrong shifted edited peaks #1443
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Demo video for fixed version Screencast.2023-07-31.14.08.58.mp4 |
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Co-authored-by: Lan Le <lan.le@kit.edu>
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Squashed commit of the following:
commit 97cf66f0ecd7427a4960d6b2d5c078a5a3e3b6e0
Author: Mehreen Mansur <mehreen.mansur@gmail.com>
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 <mehreen.mansur@gmail.com>
Date: Thu Feb 1 11:28:37 2024 +0100
feat: add helpdesk link in header (#1713)
commit 6a6c3aa6a16a849ed0fd748df704f3b814df4fb4
Author: f-idiris <112618970+f-idiris@users.noreply.github.com>
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 <55552142+adambasha0@users.noreply.github.com>
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 <pierre.tremouilhac@kit.edu>
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 <pierre.tremouilhac@kit.edu>
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 <pei-chi.huang@kit.edu>
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 <chia-lin.lin@kit.edu>
Refs: #1712
commit 5daa9eb5e84fa244e32de29615316739233f9724
Author: f-idiris <112618970+f-idiris@users.noreply.github.com>
Date: Wed Jan 31 09:28:55 2024 +0100
feat: enable nmrium in read only collection (#1708)
commit 587ee7e1248c10ea83a35bfb7a6c89eb3a75f32e
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <pei-chi.huang@kit.edu>
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 <chia-lin.lin@kit.edu>
Refs: #1711
commit d6f881903c5300129b6a44dfbd7d41acce183b29
Author: f-idiris <112618970+f-idiris@users.noreply.github.com>
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 <Christian.buggle@web.de>
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 <basha.adam@kit.edu>
Refs: #1548
commit 318fd345d60a2d0419bcf0faf5c2ce058f4ad8af
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
commit 4ac32c73d2d004962afca7e4fe113ff12e667b9d
Author: Pei Chi Huang <pei-chi.huang@kit.edu>
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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
commit f0d6f7b90e114eb999d81918fa350ea65e9eaadd
Author: Christian Buggle <Christian.buggle@web.de>
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 <59936007+mekkyz@users.noreply.github.com>
Date: Wed Jan 24 10:30:07 2024 +0100
fix(UI): sample entry label alignment (#1693)
commit d60d9f7958b14bca76266e763b94d8663c7e4e49
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <baolan2005@gmail.com>
Date: Wed Jan 24 09:21:27 2024 +0100
feat: update react-spectra-editor to display theoretical mass value
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1675, https://github.com/ComPlat/react-spectra-editor/pull/186
commit c69bbf00bb5a8c9bd6614eb979f1293a172ecbc8
Author: Jan C. Brammer <jan.c.brammer@gmail.com>
Date: Wed Jan 24 09:03:36 2024 +0100
feat: Add `variations` attribute to reaction report settings (#1697)
commit e51e89d8d3f960aee5bcfdc989cb061198063af3
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <jan.c.brammer@gmail.com>
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 <59936007+mekkyz@users.noreply.github.com>
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 <jan.c.brammer@gmail.com>
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 <pei-chi.huang@kit.edu>
Date: Thu Jan 18 15:07:30 2024 +0100
fix(int): zip upload
Co-authored-by: Chia-Lin Lin <chia-lin.lin@kit.edu>
Refs: #1690, #1688
commit 9a765180670bd9c737630ac31668786adf6026aa
Author: Lan Le <baolan2005@gmail.com>
Date: Thu Jan 18 09:52:35 2024 +0100
test: fix stub request in spectra jdx test
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1689, #1596
commit 1a93cf52ceac1eed19d2ffc50c62c4528531df0e
Author: Pei Chi Huang <pei-chi.huang@kit.edu>
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 <chia-lin.lin@kit.edu>
commit 69ad0a9ad183a9d614489a1ea38a47f82895b6b1
Author: PiTrem <pierre.tremouilhac@kit.edu>
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 <baolan2005@gmail.com>
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 <lan.le@kit.edu>
Co-authored-by: PiTrem <pierre.tremouilhac@kit.edu>
commit 5bee5403e369abd63a2fcb64ff7e46dcef98a9fd
Author: Jan C. Brammer <jan.c.brammer@gmail.com>
Date: Wed Jan 10 15:47:09 2024 +0100
fix: temperature conversion in reaction
Refs: #1680
commit 4c7b2ff43a2025c7a92f4319b3d1181366e94010
Author: Mostafa Mekky <59936007+mekkyz@users.noreply.github.com>
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 <fmauz@ipb-halle.de>
Date: Wed Jan 10 09:08:50 2024 +0100
fix: tests for searching cell lines (#1678)
commit a0c1b34399cc31fccd0263d1c7d194fb8dad4189
Author: f-idiris <112618970+f-idiris@users.noreply.github.com>
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 <fmauz@ipb-halle.de>
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 <bq@megorei.com>
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 <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
Refs: #1671
commit cc3930d079d7e958f158edc860d0626df5876660
Author: Mostafa Mekky <59936007+mekkyz@users.noreply.github.com>
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 <baolan2005@gmail.com>
Date: Wed Dec 20 10:53:30 2023 +0100
fix: remove original data from nmrium data before storing it
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1661
commit 63c4e32e0441656081e13088be6ce63b5af101d0
Author: PiTrem <pierre.tremouilhac@kit.edu>
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 <baolan2005@gmail.com>
Date: Wed Dec 20 06:00:40 2023 +0100
feat: add chemspectra with ref peaks (#1596)
Co-authored-by: Lan Le <lan.le@kit.edu>
commit 589e8b8bc46bc1d17c19f2af978b5368dcef0ad5
Author: Lan Le <baolan2005@gmail.com>
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 <lan.le@kit.edu>
Refs: #1656, https://github.com/ComPlat/react-svg-file-zoom-pan/pull/44
commit df1a75b92b4f2ad3786a63810720dc81f152d080
Author: Johannes Haubold <jh@megorei.com>
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 <59936007+mekkyz@users.noreply.github.com>
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 <mehreen.mansur@gmail.com>
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 <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
Co-authored-by: mekkyz <mos.mekky@gmail.com>
Refs: #1645
commit b8cde5288c6829bce1f3accccf6d0f6dd8b8b1b1
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
Date: Thu Dec 7 08:46:27 2023 +0100
test: fix test with deviceBox sorting in inbox
Co-authored-by: Tasnim Mehzabin <tasnim.mehzabin@live.com>
Refs: #1657 , #1446
commit fed53fa6568642af069377ebe4ce4b78d70c37b9
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
Refs: #1446
commit 3752367b14fadb8f090b62e0c63a97bb3990c53e
Author: Lan Le <baolan2005@gmail.com>
Date: Tue Dec 5 15:28:23 2023 +0100
fix(spectra): order of J value
Co-authored-by: Lan Le <lan.le@kit.edu>
Ref: #1649, https://github.com/ComPlat/react-spectra-editor/pull/179
commit a87201224d7a2cc88ab9f75342c308ad3295dd8c
Author: Lan Le <baolan2005@gmail.com>
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 <lan.le@kit.edu>
Refs: #1651
commit d503a4c5fa135b808bb80c77ef82d310cb40d2e8
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
Refs: #1643
commit 97fcdd69aea585f94ac6ff62103968f8c519f181
Author: Mehreen Mansur <mehreen.mansur@gmail.com>
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 <baolan2005@gmail.com>
Date: Wed Nov 29 11:10:24 2023 +0100
fix: update chemspectra client to prevent crash on CV layout
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1637, https://github.com/ComPlat/react-spectra-editor/pull/177
commit 93f8dce78cd647cec3adb653fb7093cadecc1e74
Author: Fabian Mauz <fmauz@ipb-halle.de>
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 <55552142+adambasha0@users.noreply.github.com>
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 <m.starman@live.com>
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 <pierre.tremouilhac@kit.edu>
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 <55552142+adambasha0@users.noreply.github.com>
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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Refs: #1609
commit e3b90c636b0b1cd419f31b59ea591abafb9c9c50
Author: Lan Le <baolan2005@gmail.com>
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 <lan.le@kit.edu>
Refs: 1630
commit 8b8690d8646a9707ee8e40026b213cebbbbfa1f7
Author: Lan Le <baolan2005@gmail.com>
Date: Mon Nov 20 16:17:20 2023 +0100
fix(spectra): remove blank line when saving peak
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1629
commit e559183511e644df48ec363da9186dcc36f6eb69
Author: Pei Chi Huang <pei-chi.huang@kit.edu>
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 <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
commit a31a0ffdf84c81e6674b942f4272410431876073
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <pei-chi.huang@kit.edu>
Date: Thu Nov 16 06:41:31 2023 +0100
feat: drag samples and elements to segment (#1623)
commit c1e26a2fb8970fbf3ac54c1e40170e98f89effe2
Author: PiTrem <pierre.tremouilhac@kit.edu>
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 <basha.adam@kit.edu>
commit 09ec1599c0a17ec153b0fdc3941178f85c79a7ee
Author: Lan Le <baolan2005@gmail.com>
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 <lan.le@kit.edu>
commit 8203debbcfa84f7efb7d06021da63421b03e737a
Author: f-idiris <112618970+f-idiris@users.noreply.github.com>
Date: Tue Nov 14 12:28:20 2023 +0100
feat: report peaks from XRD (#1614)
commit da0074b4e3a585baf37698f8e6015cf624de7091
Author: Pei Chi Huang <pei-chi.huang@kit.edu>
Date: Tue Nov 7 12:30:53 2023 +0100
feat: better grouping of decoupled samples in list (#1612)
commit ab9f67a5c4ea265edcf5ae7396a160676d067fdc
Author: Lan Le <baolan2005@gmail.com>
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 <lan.le@kit.edu>
refs: #1607
commit be8e927e95f7f7383638e688ed3fa4e742a19986
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
commit c61c86a162270ff0c3a2ac5d4806d23ed40bed18
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
commit 6f1afba3a0861363e18962df96128d478647989a
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <tasnim.mehzabin@live.com>
commit 84c02bced038ef307abb67393a86a3fe71f8bb35
Author: Pei Chi Huang <pei-chi.huang@kit.edu>
Date: Wed Oct 25 09:48:20 2023 +0200
feat: converter trigger on attachment inbox items
Refs: #1583
commit 75fde46a36618f7c887408ff11628bf865a5150f
Author: PiTrem <pierre.tremouilhac@kit.edu>
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 <pei-chi.huang@kit.edu>
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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
commit 48aef3b04ae3aca429755d4da6f9550237f12e00
Author: Pei Chi Huang <pei-chi.huang@kit.edu>
Date: Tue Oct 24 10:46:19 2023 +0200
feat: expand calendar function to generic element
Refs: #1585
commit 3ef1129914dfb73b32d54b1a52cbd7b65009d7e7
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <pei-chi.huang@kit.edu>
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 <baolan2005@gmail.com>
Date: Tue Oct 10 10:11:06 2023 +0200
fix: hide spectra button when only uploading an image (#1568)
Co-authored-by: Lan Le <lan.le@kit.edu>
commit 10ef1f11cd39750ccdb72df4152dfedf6af56c44
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <pierre.tremouilhac@kit.edu>
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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
commit 3de16fa33e1bdb7eaba46c3f793fd346aca7ac83
Author: PiTrem <pierre.tremouilhac@kit.edu>
Date: Mon Oct 9 16:08:16 2023 +0200
fix: rollback labi version up (#1570)
commit 0781e5cda2d2b25a430193018ea5cf46d22799e3
Author: PiTrem <pierre.tremouilhac@kit.edu>
Date: Mon Oct 9 13:59:49 2023 +0200
prep v1.8.0-rc2
commit c4200dffad7d30f20aa0b7cb1654ba21cc11c63b
Author: PiTrem <pierre.tremouilhac@kit.edu>
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 <baolan2005@gmail.com>
Date: Mon Oct 9 13:48:18 2023 +0200
feat: update chemspectra to change value of referent solvent (#1557)
Co-authored-by: Lan Le <lan.le@kit.edu>
commit bebdec0eea8170f21a36e97f64756b0aaf84a279
Author: Mostafa Mekky <59936007+mekkyz@users.noreply.github.com>
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 <fmauz@ipb-halle.de>
commit be0bcd83da967882e3e912f2d9ed58ccf302caf6
Author: Lan Le <baolan2005@gmail.com>
Date: Mon Oct 9 12:45:08 2023 +0200
feat: show nmrium button for reaction and research plan (#1471)
Co-authored-by: Lan Le <lan.le@kit.edu>
commit ee881fefd4ce37da533db58a325687c0320e71fa
Author: Jan C. Brammer <jan.c.brammer@gmail.com>
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 <fmauz@ipb-halle.de>
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 <basha.adam@kit.edu>
commit c1b45ae4105d2d19e74b88a5761cb41eb873e128
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <baolan2005@gmail.com>
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 <lan.le@kit.edu>
Ref: #1563
commit 10d35642ccb7e11b448fd6f06164171bf75b2d7f
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <basha.adam@kit.edu>
commit 1795b4b0729e0aea14909438099db628baf20c9c
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <TasnimMehzabin@users.noreply.github.com>
Date: Thu Oct 5 07:55:25 2023 +0200
fix: current_user.matrix getting null value
Refs: #1554
commit c5c7b2faf4c7161d6e52dc4bd75ea976e1f54e4f
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <jan.c.brammer@gmail.com>
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 <TasnimMehzabin@users.noreply.github.com>
Date: Wed Sep 27 15:56:52 2023 +0200
fix: comment fetch issue on new entities
Refs: #1547
commit 9992a85878d4fb272b4fca9639b8d35f3c93f3f6
Author: Lan Le <baolan2005@gmail.com>
Date: Wed Sep 27 15:54:56 2023 +0200
chore: update chemspectra backend version to display label cv layout
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1546
commit ba6c1d9af0334da5a86c23d14e64714e0fe3a7f7
Author: Lan Le <baolan2005@gmail.com>
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 <lan.le@kit.edu>
Refs: #1526
commit 1a9fc9e730f24ffed42ef928b3938693a47e47ff
Author: PiTrem <pierre.tremouilhac@kit.edu>
Date: Fri Sep 22 13:23:25 2023 +0200
fix: wrong conflict resolution (#1542)
commit fc4bf31e40400f43c88604a36396b886f6ef073e
Author: PiTrem <pierre.tremouilhac@kit.edu>
Date: Fri Sep 22 09:00:35 2023 +0200
test: update runner image (#1541)
commit 154e18cea48ddd3b4c1c7b45623d16d501ca59a9
Author: Mostafa Mekky <59936007+mekkyz@users.noreply.github.com>
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 <pierre.tremouilhac@kit.edu>
Date: Wed Sep 20 07:19:47 2023 +0200
chore: prep v1.8.0-rc1
commit 98665123f0ab527ee71537eef2e0b3c43c9d1d69
Author: Pei Chi Huang <pei-chi.huang@kit.edu>
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 <chia-lin.lin@kit.edu>
commit 728e95ff4388fd9cb34e2bd6b582e1fd341e952b
Author: PiTrem <pierre.tremouilhac@kit.edu>
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 <jan.c.brammer@gmail.com>
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 <59936007+mekkyz@users.noreply.github.com>
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 <jh@megorei.com>
Date: Wed Sep 20 06:54:49 2023 +0200
feat: Move sample task inbox to header bar
Refs: #1517
commit dc4283bbd6c15d12fd27fc42f157eb465e29d882
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <pierre.tremouilhac@kit.edu>
Date: Wed Sep 20 06:48:58 2023 +0200
chore: prep v1.7.3 (#1537)
commit ff9b54715e5a7620609593996dff6a56eaf2ea02
Author: PiTrem <pierre.tremouilhac@kit.edu>
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 <pierre.tremouilhac@kit.edu>
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 <jan.c.brammer@gmail.com>
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 <jh@megorei.com>
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 <md@megorei.com>
commit 40bc206fb0aeff7c6aad6bdec75259af53fad571
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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 <112618970+f-idiris@users.noreply.github.com>
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 <baolan2005@gmail.com>
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 <lan.le@kit.edu>
Refs: #1528
commit 74215ebd0dceac135e845933c5dfc53021e35e30
Author: Lan Le <lan.le@kit.edu>
Date: Fri Sep 1 12:00:45 2023 +0200
fix: check the nmrium file before ignore generate
commit d8ba70f0743cfe99bbaba2591ed9fbbb4e47947e
Author: Lan Le <lan.le@kit.edu>
Date: Mon Aug 28 14:37:19 2023 +0200
feat: update chemspectra frontend to fix bugs
commit 03b28ce207b5de6e29582550efc0d5467ba9bf0a
Author: Lan Le <baolan2005@gmail.com>
Date: Fri Aug 25 13:16:47 2023 +0200
fix: ignore predictions when it is null
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1507
commit 81ad5d081112111bd38f72ac0042bb0fa7ba80be
Author: Fabian Mauz <fmauz@ipb-halle.de>
Date: Fri Aug 25 12:34:10 2023 +0200
fix: fixed wrong literatures mapping
Refs: #1506
commit e29301f949fba54748b70116b0016b698cc0f60b
Author: Fabian Mauz <fmauz@ipb-halle.de>
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 <pierre.tremouilhac@kit.edu>
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 <jan.c.brammer@gmail.com>
Refs: #1489
commit 37acd1675050e0b76b4e0bd3e738e8dd224f1c5f
Author: Fabian Mauz <fmauz@ipb-halle.de>
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 <TasnimMehzabin@users.noreply.github.com>
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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Refs: #1488
commit 4e781496197cc604800b4470fcff3b872902e13e
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <baolan2005@gmail.com>
Date: Thu Aug 24 08:52:12 2023 +0200
fix(spectra): sorting multiplicity values
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1478
commit 9ea494f22a6602692cd3dfae6fd59a0634e6bdc4
Author: f-idiris <112618970+f-idiris@users.noreply.github.com>
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 <jh@megorei.com>
Date: Tue Aug 22 10:36:44 2023 +0200
fix: replace toSorted with manual sorting in SampleTaskInbox
Refs: #1485
commit 5d2cf58096137571fe83c81ff247952f89b7f790
Author: Lan Le <baolan2005@gmail.com>
Date: Fri Aug 18 09:53:10 2023 +0200
feat: update version of chemspectra
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1480
commit 0735f723302fb5cd12cb43abafad581a91e631ae
Author: Lan Le <baolan2005@gmail.com>
Date: Fri Aug 18 09:51:13 2023 +0200
chore: update information of chem-spectra-app
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1484
commit f75d55439f856b4f7e2dfffee3d2fbf2f2bcd4f6
Author: Lan Le <baolan2005@gmail.com>
Date: Thu Aug 17 15:57:35 2023 +0200
fix: hide NMRium button on non-NMR layouts
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1460
commit aa30d087c328af7d210074bd671fd3b0c9375892
Author: Lan Le <baolan2005@gmail.com>
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 <lan.le@kit.edu>
Refs: #1436
commit 8347fe8e145aa56773725e78626693bd5a727329
Author: Mehmood Ghaffar <engr_mehmood86@hotmail.com>
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 <jan.c.brammer@gmail.com>
commit 412899294a67832fcbb6fba8179adb78fa770695
Author: PiTrem <pierre.tremouilhac@kit.edu>
Date: Tue Aug 15 10:11:35 2023 +0200
chore: update README - acknowledge NFDI4Chem
Refs: (#1472)
commit 98a50308a03e80d6716dedebdf7c38d25f6b9092
Author: Mostafa Mekky <59936007+mekkyz@users.noreply.github.com>
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 <59936007+mekkyz@users.noreply.github.com>
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 <baolan2005@gmail.com>
Date: Thu Aug 10 16:08:32 2023 +0200
feat: add Emission, DLS ACF, DLS intensity layouts
Co-authored-by: Lan Le <lan.le@kit.edu>
Refs: #1374
commit 9ca632a4ebfe8e7a22358812880dbd94d4dbe3cc
Author: Mostafa Mekky <59936007+mekkyz@users.noreply.github.com>
Date: Thu Aug 10 13:40:11 2023 +0200
style: add-analysis button always visible
Refs: #1465
commit ecf57bea92255ed39b190afb8f6a830aa93c3b4c
Author: Fabian Mauz <fmauz@ipb-halle.de>
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 <pierre.tremouilhac@kit.edu>
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 <pierre.tremouilhac@kit.edu>
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 <jh@megorei.com>
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 <pei-chi.huang@kit.edu>
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 <pei-chi.huang@kit.edu>
Date: Wed Aug 2 15:29:24 2023 +0200
chore: upgrade convert 1.0.0
Refs: #1450
commit 2467be7906c759a3ab136109edcd9bb44e3e4ff6
Author: Johannes Haubold <jh@megorei.com>
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 <pierre.tremouilhac@kit.edu>
Date: Tue Aug 1 13:20:41 2023 +0200
fix(UI): missing generic element icon
commit f6148e650c66c21b7d3d7acf86cc5391000106cf
Author: PiTrem <pierre.tremouilhac@kit.edu>
Date: Tue Aug 1 12:06:44 2023 +0200
chore: prepare v1.7.2
commit 2d8e2fabd621dcc0a00e3d0c5291a770c070006f
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <TasnimMehzabin@users.noreply.github.com>
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 <baolan2005@gmail.com>
Date: Mon Jul 31 15:48:11 2023 +0200
fix display wrong shifted peaks after zoom (#1443)
Co-authored-by: Lan Le <lan.le@kit.edu>
commit cd4048efb5341a5362b98d41538f4509db1092a1
Author: PiTrem <pierre.tremouilhac@kit.edu>
Date: Wed Jul 26 11:57:18 2023 +0200
chores: VERSION
commit 05acee669233a93dc63b897af2e350a02dcd2f90
Author: PiTrem <pierre.tremouilhac@kit.edu>
Date: Fri Jul 21 15:26:58 2023 +0200
chores: clean stylesheet from plugin integration remnant
commit cd9b7132d1d28b862a6da3dbba434f5c18a376a0
Author: Mehreen Mansur <mehreen.mansur@gmail.com>
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 <pierre.tremouilhac@kit.edu>
commit 3cae2fdd95153dfe91ed9d6ed40a82a9456191a1
Author: Mehreen Mansur <mehreen.mansur@gmail.com>
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 <TasnimMehzabin@users.noreply.github.com>
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 <baolan2005@gmail.com>
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 <lan.le@kit.edu>
commit baa6a4fa9f15068115465fb9e2b4d203f294b865
Author: Mehreen Mansur <mehreen.mansur@gmail.com>
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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
commit 313f34222c836a2eff72623653b14e49eae0d872
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
commit ee68158d7973acfc5b8deedf2c41ce0715ff7fb7
Author: TasnimMehzabin <TasnimMehzabin@users.noreply.github.com>
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 <112618970+f-idiris@users.noreply.github.com>
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 <112618970+f-idiris@users.noreply.github.com>
Date: Mon Jul 17 09:42:35 2023 +0200
fetch attachment preview for new attachments only (#1410)
commit b82e7222cf47460a92a08e547035d3e128bcb3f7
Author: Mehreen Mansur <mehreen.mansur@gmail.com>
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 <pierre.tremouilhac@kit.edu>
commit 77f83bfd132101bd69efec380923f9ad47e7aa94
Author: Adam Basha <55552142+adambasha0@users.noreply.github.com>
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
added a commit
that referenced
this pull request
Mar 5, 2024
Co-authored-by: Lan Le <lan.le@kit.edu>
PiTrem
deleted the
1442-edited-peaks-are-shifted-wrong-in-some-case-on-chemspectra
branch
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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