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chore: Bump tar from 6.1.11 to 6.2.1 #95

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@dependabot dependabot bot commented on behalf of github Apr 11, 2024

Bumps tar from 6.1.11 to 6.2.1.

Release notes

Sourced from tar's releases.

v6.1.13

6.1.13 (2022-12-07)

Dependencies

v6.1.12

6.1.12 (2022-10-31)

Bug Fixes

Documentation

Changelog

Sourced from tar's changelog.

Changelog

7.0

  • Rewrite in TypeScript, provide ESM and CommonJS hybrid interface
  • Add tree-shake friendly exports, like import('tar/create') and import('tar/read-entry') to get individual functions or classes.
  • Add chmod option that defaults to false, and deprecate noChmod. That is, reverse the default option regarding explicitly setting file system modes to match tar entry settings.
  • Add processUmask option to avoid having to call process.umask() when chmod: true (or noChmod: false) is set.

6.2

  • Add support for brotli compression
  • Add maxDepth option to prevent extraction into excessively deep folders.

6.1

6.0

  • Drop support for node 6 and 8
  • fix symlinks and hardlinks on windows being packed with \-style path targets

5.0

  • Address unpack race conditions using path reservations
  • Change large-numbers errors from TypeError to Error
  • Add TAR_* error codes
  • Raise TAR_BAD_ARCHIVE warning/error when there are no valid entries found in an archive
  • do not treat ignored entries as an invalid archive
  • drop support for node v4
  • unpack: conditionally use a file mapping to write files on Windows
  • Set more portable 'mode' value in portable mode
  • Set portable gzip option in portable mode

... (truncated)

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Chemotion and others added 22 commits January 16, 2024 11:07
In short:
- data submission feature added to user ELN page
- Review page for internal reviewing
- Public page to browse published sample/reaction data

Contributors:
Chia-Lin Lin
Pei-Chi Huang
Pierre Tremouilhac
* add xvial and type check

* readonly for nmr

* trim data from orcid

* refresh embargo list

* add a button to redirect from db view to publication view

* export-sample-with-https-doi

* add loading module on publication search

* collection label error

* download analysis of publication without sign in

* view sprectra of products

* orig. is not required

* export embargo collections

* search embargo bundle number

* display name on review page

* embargo in reaction list

* search by authors or contributors

* sanitize_sql

* allow users to edit spectra's content

update package

using chem-spectra-client version 0.10.11

update version of chem-spectra-client

* deploy config mod

* add xvial symlink

* minor upd  Gem.lock db/schema

* add default profile

* FE fix after rebase

* update style back to original setting

* use 'mass spectrometry' and 'IR'

* publication embargo search

* make regenerate button for all unoriginal jdx files

* regenerate for reviewer only

* check and fix

* smiles to SMILES

* add permission on repository_api reaction and sample

* add validation

* fix migration file for solvent

* review reaction scheme

* fix duplicate function name from ELN rebase; publish reaction

* reaction list style

* focus on style of review page

* publication molecule layout

* add publish date to new layouts

* change style to solve overlap issue

* directing to the sample of publication
change wording 'xxx DOI' instead of 'DOI'

* fix e.split on review page issue

* fix e.split on review page issue

* review submitter list issue

* publication author and the link

* 1. unify the terminology: use Reference(s)
2. define citation type
3. publish references

* move js file to packs

* bundler

* migration file

* rm chemscanner

* chemscanner

* submission validation and collection

* reference desc

* rm dup. decoupled

* ref

* spectra 0.10.14-beta.0

* Collection DOI

* display the latest image

* Collection DOI

* Resolve "upgrade datacite schema"

* nmrshiftdb solvent

* add 'copy to clipboard' on collection doi

* assign to embargo

* Resolve "publish when segment exist"

* att permission for seg

* default segment of reaction, segment for publication

* oai metadata

* submission date

* option to skip yield validation

* how-to link and quill-viewer styling

* 1. add a button to copy collection DOI
2. add a checkbox confirmation to ensure that people that add data without an embargo know that the data is published as soon as review is completed

* reviewer-permission-with-embargo-accepted

* metadata

* remove regex of orcid in frontend
get result from API directly

* link to publications by clicking on the statics

* review comment

* the focus is on the selected record in the list when redirecting from a DOI

* switch tab after searching by inchi

* review comment r

* added molecule archive

* add xvial filter

* add xdata to the list

* count of compound

* publication element index

* import collection

* embargo author

* rename terms of service to directive

* landing page updates:
1. the word 'published' next to the analyses (right side) should be given in black.
2. add a published link to the samples (left side)
3. in reaction table
- space in header between name and unit
- unit in squared brackets
- ml should be mL
- switch from g to mg as unit
- bring yield in the sub header of the table

* new content of project description of about

* update copyright statement

* linting

* fix hyperlink as string issue

* fix dataset doi cannot be resolved issue

* add embargo link on review and copy function

* fix the bug for hyperlink export

* fix routing

* fix collection routing and info modal

* fix based on feedback

* workaround for react-svg-file-zoom-pan-latest library issue

* chem converter

* fixed: redirect to the latest published element successfully, but no details shown

* review comment fix

* hide info when inchikey is dummy

* embargo btns

* hr to h

* Update Navigation.js

* converter for user

* converter config file

* embargo email issue

* upgrade chemspectra

* fix duplicated img

* Resolve "porting the 3d viewer"

* Revert "Merge branch '520-upgrade-chemspectra' into 'server_chemotion_net-5'"

This reverts merge request !471

* upgrade chemspectra

* fix duplicated img

* embargo job fix

* disable 3d molecule

* publication page issue

* fix file ext issue

* resourceTypeGeneral sample

* add example text on request form

* increase font size

* ketcher backend

* add nmrium aasm_state 

so that files with this state from ELN v1.5 can be transferred  (avoid `ActiveRecord::RecordInvalid (Validation failed: Aasm state is invalid)` on attachment save `app/api/chemotion/gate_api.rb:167` )

at this stage no event seems to be needed

* metadata description of sample publication

* sample representation on landing page

* shibboleth and group leader review

* Resolve "sync spectra"

* review notification

* Resolve "molecular mass descriptor in sample metadata"

* group default value

* fix White Screen when clicking on Analysis DOI

* fix white page while doi is null

* fix the incorrect license icon usage

* user reivew and svg fix

* group lead review update

* increase font size and add space

* add comp-number to published sample page

* Resolve "review ui reload issue"

* Resolve "compounds visibility"

* anchor on publication page

* add solvent to sample metadata

* published year

* linked-data

* add original id to compound list

* linked data api

* Extending chemotion_ELN with Repository functions

In short:
- data submission feature added to user ELN page
- Review page for internal reviewing
- Public page to browse published sample/reaction data

Contributors:
Chia-Lin Lin
Pei-Chi Huang
Pierre Tremouilhac

---------

Co-authored-by: Chia-Lin Lin <[email protected]>
Co-authored-by: Pei-Chi Huang <[email protected]>
Co-authored-by: Lan Le <[email protected]>
Co-authored-by: PiTrem <[email protected]>
remove download zip button
fix font size analys content description
add bottom nav bar
revamp top navbar

pubchem tag in public molecule list

enable search for unsigned user

public search

suggestionapi set var if no current user for public coll

BE: search_api: serialized result for public molecule

FE: public store receive search result too

disable groups UI

fix Nav header in ELN view

navbar: remove search/element actions for non sample/react elements

change routing

revamp style for publication list/element
change routing  to publication/molecules/:id

refact href to onClick

change route root to pages (nginx dual site)

welcome routing

enable user devise confirmable

FE publish sample: fix missing argument

public api inchikey
add params validation
default analysis version to 1 if no version while comparing with params version

fix sample publication
-- reintroduce analyses selection for publication (broken thru dnd analyses reordering)
-- fix coauthor id (broken thru reactselect upg)

change default check analysis selection for sample publish

publish analyses default checked using null and true instaed of boolean becasue the extended_metadata value is coerced into string

fix attachment copy

fix publish doi/pubchem
fix sample dataset versioning for doi token
loop throug sample publication tag for authors and affiliations

implement new datacite schema
revamp publication concern

upg upd pubchem tag thru sample

dedicated publication logger

allow collection array arg in CollectionSample.create_in_collection

Sample publication Datacite/Pubchem
split process into distinct DJs

fix search suggestion on publications page when logged

WIP revamp PublishSampleModal

WIP

f job move to final collection

f

reverse kind analysis options

wip publication tag +revamp

welcome page upd last sample view with new publiation tag struct

disabled checkbx analysis selection if already published

tag analysis as published in extended_metadata column

fix route for analysis kind having white space

f

pick 818eff6 REPO FACTOR
s 760b833 remove download zip button fix font size analys content description add bottom nav bar revamp top navbar
s 7db9740 pubchem tag in public molecule list
s 40059a3 enable search for unsigned user
s 08c12d2 disable groups UI
s 4e939a9 change routing
s e244e47 enable user devise confirmable
s 2fc9ee6 FE publish sample: fix missing argument
s 64f8cdd fix attachment copy
s d48bf69 fix publish doi/pubchem fix sample dataset versioning for doi token loop throug sample publication tag for authors and affiliations
s c1bd3b7 upg upd pubchem tag thru sample
s 0cf8dd8 dedicated publication logger
s 2fab086 allow collection array arg in CollectionSample.create_in_collection
s 74f8d4d Sample publication Datacite/Pubchem split process into distinct DJs
s 7f97cc9 fix search suggestion on publications page when logged
s aaec7c1 WIP revamp PublishSampleModal
s 6389a27 WIP
s c76de3b f job move to final collection
s d245e57 f
s 403cee5 reverse kind analysis options
s 4498f05 wip publication tag +revamp
s 0ca4452 welcome page upd last sample view with new publiation tag struct
s b725bec disabled checkbx analysis selection if already published
s b02fdf1 tag analysis as published in extended_metadata column
s c009c22 fix route for analysis kind having white space
s 7b12b5c f

hide collection management button

hide shared & sync collection selection trees

fix private method container publication

add molecule name to public sample detail view

sort molecules in public collection

add publishedTag to samples in  user sample lists

add doi link to publication tags of published elements in ELN view

hide create new collection in moving/assigning elements modal

User Collections fixes

hide user own collections
do no create a locked 'chemotion.net' collection for new user
but instead  'ELN Gate' and 'My Data'

mv chemotion label to publish common

tag published molecule with doi too

chemotiontag revamp

change ELN navbar color to gradient

up collection tree

nav bar font white

register repo token into eln for gate data transfer

remove gradient nav bar

btn-unified class

sample export xls: exp chemotion doi tag if present

fix origanization input: disabled to readonly

fix missing sync collection for new user persons

correct updating chemotion molecule tag

publication detail restyle

xls export analyses doi

fix analysis publish checkbox:

reload sample after publish

fix checkbox toggle

log analyses selection to publish

log WIP disable publish api

https doi metadata

upg sync_coll entity for public collections

upd Terms n Conditions

categorize literatures for pulbicl collection elements

persons can add references to public elements through
literature managmt panel as for their own elements
ref are categorized as 'public'

list public literature in element detail view

f

display cited literature wiht referer in public publication list

fix lit flux api

add doi table/model

fix checkbox add analyses to publish

do not backup uploads

doi reservation : fix doi model routine

fix displaying published molecule associated to published samples missing their publication tag

fix bug from attachment polymorphism upgrade

publish UI add accordeon

rework doi model, publication concern

mv publish button to publishCommon, disable btn when already published

serialize user affiliation

unassociate analyses doi if inchikey changed

popover information for doi reservation

upd doi seeding

DJ params fix fatal: hash keys cannot be integer: stringify analyses id

log DC metadata xml to upload as separate files in log/

WIP

fix pannel after bootstrap upg

fix pagination after bootstrap upg

fix ci

root page link to chemscanner

publish reaction UI completed

backend code complete, but still need testing (especially doi part)

add published button on reaction list and header

re-add LabelPublication on header

fix the username display issue

public reaction backend

db/schema

f

fix do not expect new reaction to have tag data

move publish sample/reaction out of sample/reactionAPI to dedicated repo api

fix anonymous search

reactionPublishBtn upg

publishBtn: workaround with overlaytrigger on disabled Btns

publish reaction btn on publishable reactions

mount repositoryAPI

clean repoAPI

do not uses sample.analyses but sample.container

publish analysis: fix checkbox toggle

bootstrap fix table props

repo publishmodal fx panel-group assistech prop warning

reaction publish btn: disabling/tooltip message upg

reactionPubModal fx warning iter key

green header for public detail panel &  welcome page upg:

- in ELN view, elemt detail panel has green header instead of blue if elemt is public
- rm directive content iframe, use component instead -> NB this duplicate the info
- footer upg
- rm footer from publications page
- rm osadl partner card
- change institute link to brase group
- change banner color/font

repository search

hide reaction publishbtn

disable reaction publication api

add chemotion logo on welcome page

fix sample doi fetcher analyses filter

mv publish actions/fetchers to dedicated classes

repo api mv helper

repo_api upg

repo api fix

clean deprec residual react.proptype

f

search api fx to work on public page when logged in

repo api wip

FE fix iterator uniq key

repo_api wip

WIP

publish sample JOB upd

WIP_pubreact_DRY

DRY FE repository fetchers

reaction inchi routines for product only rinchi

publish reaction: duplicate reaction BE logic

reaction publish tag

DJ reactionpublish

repo api fix

deletejob

f_job

f_job

f_dj_publish

f_DJ

show publish reaction btn

fix replacmt ElementActions by RepositoryActions

reaction svg composer pass options

disable green chemistry tab

DJ publish fx

sync public collection for new user: allow reaction details

f

fix dois generation when count > 10

update molecule tag: only for sample not reaction

fix xml metadata reaction

DJ publish reaction fix

hisde pub reaction btn for public reaction

repo_api reaction fix

publish reaction prepare prod

public reaction detail panel green header

doi redirect simplified

routing redirect from reaction dois

ELN: error when att.copy => rm include  attachment concern assm/JCAMP

WIP reaction list view

add Formula

Reactant and starting material should not in publications

Add conditions to filter out the sample which is as
starting material/reactant in reaction.

If a sample is published as 'Sample', it will be shown on the
publication list.

If a reaction is published, the 'Product'(sample) will also be published
and shown on the publication list. The 'starting material' and 'reactant'
will not be shown on the list.

BE/FE fetch reaction list

f

Affiliation output: rm group from affiliation

publications table: add original element

WIP revamp job chain

toggle for sample and reaction search

reaction page

Publication: added ancestry

fix search_by_method and remove wellplat and screen codes

Create Publication entries w ancestry for each element

- rev duplicate anaylses container

revamp xml metadata files

WIP new publishing process job

Publishing job

pseudo state machine for Publication model
added transition in Publication model

todo: clean element tagging, doibag, xml metadata

fix

WIP FE check taggable_data of publication

repo_api fx

add 'reaction/' to reaction doi suffix
remove html formatting from doi metadata

search

fx publishing pubchem registr

routes fixes

doi link

deploy config

fix routes

doi url

redirect reaction

fix sample publish

the latest publish sample on landing page

set publish switch button size and position

Publication Rinchi fixed

reaction detail 10

reaction additional info backend

Additional information on publication reaction

Add:
1. Expand/Collapse RInChiKey information
2. Status, Start, Stop, Duration, Temperature, Additional information
for publication and purification details
3. TLC-Control information

Publications analyses re-layout

Relayout the Sample and Reaction on publications. The details are as
below:

- Reaction
1. Remove title (Short Label/Name) from Reaction

- Sample
1. Remove Reaction data from Sample

- Sample and Reaction
1. Rename 'Datasets' as 'Analyses'
2. Expand/Collapse analyses at one click
3. Remove the outer(the first layer) border

- Datasets
1. Expand/Collapse analyses at one click

remove RenderAnalysis

published reaction literature display

provided a reaction link on sample detail for publication

Analyses types in one line

User can expand/collapse analyses list by clicking analyses list header.
The types are listed together on the header and separate with ','. Also
put the symbol in front of the type(s) to indicate its Sample or Reaction.

Analyses preview function

When user click on the preview image of analyses, display the original
image for user.

This function is available only when user sign in already. If user
click the preivew but he/she does not sign in, a system notification
shows up in the top center to remind him/her 'Please sign in first'.

Additional updates on:
1. Only import the one which is used from 'lodash', not import all from 'lodash'
2. Remove unused imports
3. Add semicolon

Analyses format

Align UI elements.
Add some styles to make analyses more readable.
When user double click Content, more space is added and looks like it
is expanded. Fix by removing the theme setting on render.

Reaction in the centre and remove start stop

Remove 'float: left' to set reaction image in the centre of reaction
list.

Remove 'Start' and 'Stop' information.

Use Div instead of FormControl to make the TLC-Description looks not
like an input column.

Rename some panel id, e.g. use 'collapsible-panel-rinchis' instead of
'collapsible-panel-example-1'.

Console warning about unique key and inline

Add 'key' pop and inline='true' to fix below warnings:
1. Warning: Received 'true' for a non-boolean attribute 'inline'
2. Warning: Each child in an array or iterator should have a unique 'key' prop

Public pagination and duplicate molecules

When user uses switch button to list samples or reactions, the pages
need to be calculated by samples or reactions.

Additional:
When user uses 'Search', e.g. input inchistring and then search, the
duplicate molecules show on the sample list and the pages go wrong.
Fix this by using '.uniq' on api and 'molecules.size' for totalElement.

repository scheme

fix redirect

fix doi suffix generation for reaction duplicate

Reaction doi route

Add .version if the version exists.

Test on local environment:

1. With http://localhost:3000/inchikey/reaction/SA-FUHFF-UHFFFADPSC-UHFFFADPSC-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ,
it goes to Reaction id 22.

2. With http://localhost:3000/inchikey/reaction/SA-FUHFF-UHFFFADPSC-UHFFFADPSC-UHFFFADPSC-NUHFF-NUHFF-NUHFF-ZZZ.1,
it goes to Reaction id 23.

3. With http://localhost:3000/inchikey/RJQVSFJIBQPCLA-UHFFFAOYSA-N,
it goes to Molecule 1287.

4. With http://localhost:3000/inchikey/RJQVSFJIBQPCLA-UHFFFAOYSA-N.1,
it goes to Molecule 1287.

scheme issue fix and layout

Disable reaction publish button after publish

After user use publish button to publish a reaction, this button should
be disabled so user can not publish the same reaction again.

The render() of ReactionDetails is not triggered properly when state is
changed, so the UI remains the same and does not display correctly with
the latest data. Use forceUpdate() to force execute the render().

fix sample doi reservation

disable sample publish button after publish

Add scroller and toggle panel into publish reaction modal

Add scroller into publish reaction modal so the user can scroll up and
down to view the publish details. Some styles are added to fit the modal.

Add toggle function on RInChiKey, Properties. and TLC.

Additional:
Eliminate some ESLint warning, e.g. use textAlign not text-align,
className not class, fontSize not font-size...etc.

sample publish after update

sample reserve dois spinning icon

Toggle panel into publication reaction

Add toggle on Analyses of publication reaction; publication sample also.

hide ManagingAction share-button

Reaction Reserve DOIs

in landing page add link to spectraviewer

migrate legacy published samples/analyses to table publication and sorting the taggable_data

publish sample and reaction analyses check

rm secrets for testing

publication page description disable when no data

analysis sorting

fx_task

Analysis preview for the public

The public can preview the analysis image, no need to sign in the
system.

Summary:
1. copy publication image file to public folder when doing duplicate
datasets and copy attachments
- The file path format is 'public/images/publications/{attachment.id}/{attachment.filename}'.
- Copy the one which will be in table: publications, not the original ones.

2. fetch image file from public folder if the user is from the public, otherwise,
use the the original api which gets the image file from store
- If the fetch file fails, use thumbnail instead so user will not get any system error.
And we are aware that the image file does not exist in public folder from console log.

3. one-time task 'ver_20190128000004_copy_image_to_public' is created
- Use this task to copy the image files to the public folder. It fetches
the image files from table: publications with state='completed' and
element_type='Container' and then copy to public folder.

4. Add preview function on Dataset

Gemfile upgrade

Publication Review Process

upd mail config/development

enable reaction publishing

fix reviewing button visibility and api

mv state logic to job fix typo

reaction publication author display issue

publish check

reaction analysis publish

fix

change link to new repo hostname

New Chemotion landing page

notification for reaction and sample publish

enable cap deploy slack notification

root page: text change for link to repo

url link updates in publication mailer message

root page link to dev repo

lit api fix

lint_js

WIP_analyses_selection_checkbox_issue

typo analysis type options

fix for retracted publication

fix routing that cause break page

add last publish reaction to previous layout version

reaction and sample publish analyses checkbox issue

update publish_at

repo page routing

update deploy config

publication review

f_typo

routes and review

fix review page with literature

manual reject publication

News

Two new environment variables: ARTICLE_EDITOR, ARTICLE_PATH
E.g. ARTICLE_EDITOR: '2,7'
(user.id = 2 and user.id = 7 have the auth. to create/edit the article;
if this variable does not exist, no one are allowed to create/edit articles )
E.g ARTICLE_PATH: 'public/newsroom/'
(the stroge path for article content;
if this variable does not exist, the code will use 'public/newsroom' as default)

One new table: articles (refer to migration file)

One new gem: Moneta (refer to Gemfile)

Please refer to GitLab #148 for the UIs and details.

analysis-by-product-on-repository-page

element to review collection

change-scollection-to-collection-for-the-icon-link

disable-repo-qrcode-function

View comment with full screen size

8 fils are committed, including 2 new files:
'ReactionDetailsRepoComment.js' and 'SampleDetailsRepoComment.js'.

'ElementDetails.js', 'ReactionDetails.js' and 'SampleDetails.js'
are more ELN related and are changed to control the comment page on/off.
There other files are more Repository related.

doi report

reload fix

Fixed 'edit is not working' issue; new timeline layout of news index page

symlink newsroom for deploy

fix reaction display when reaction has no analyses

Fix by not to nest DOM elements directly under Nav component

gem upg

Js warning about id, key, expanded props and validateDOMNesting

Eliminate the javascrip warning below (when loading Sample or Reaction
in respoitory)
1. Warning: Each child in an array or iterator should have a unique
'key' prop.
2. Warning: Failed prop type: The prop id is required to make
 accessible for users of assistive technologies such as
screen readers.
3. Warning: validateDOMNesting(...): Whitespace text nodes cannot
appear as a child of <tbody>. Make sure you don't have any extra
whitespace between tags on each line of your source code.
4. Warning: Failed prop type: You have provided a  prop to
 without an  handler prop. This will render a
read-only field. If the field should be mutable use .
Otherwise, set .

responsive page for mobile

doi download fix

How-To functionality

Similar to function: Newsroom, only the different look. So the data is
stored in public folder as one index file and the others for content.
The new environment variables are added. There is no default cover image
file for How-To, use css instead.

Two new environment variables: GUIDANCE_EDITOR, GUIDANCE_PATH
E.g. GUIDANCE_EDITOR: '2,7'
(user.id = 2 and user.id = 7 have the auth. to create/edit the How-To article;
if this variable does not exist, no one are allowed to create/edit How-To articles )
E.g GUIDANCE_PATH: 'public/guidance/'
(the stroge path for HOW-To article index and content;
if this variable does not exist, the code will use 'public/guidance' as default)

Move some codes to RepoCommon for common use.

How To: reword Guidance to HowTo

Guidance -> HowTo
guidance -> howto
GUIDANCE -> HOWTO
GUIDACNE -> HOWTO

ArticleAPI: fix  user validation

add overlay

ChemDoodle molfile cleaning task

bcc reviewer

Set default route to welcome page, no matter user sign in or not

Notification/mail to submitter after review: content change

do not show 1H NMR check at public analysis

prevent app breaking

default to root page

reduce  font size lnading page panel

display reaction.duration if there, otherwise, display (end_time - start_time); fix blank page issue when user copy reaction and then publish in one move

config/deploy/howtox

Js warning on review page and published reaction

Fix the warnings below:
1. Warning: Received 'true' for a non-boolean attribute 'striped'.
If you want to write it to the DOM, pass a string instead: striped='true' or striped={value.toString()}.
    in tbody (created by RepoReview)
also: bordered, hover

2. Warning: Failed prop type: You have provided a expanded prop to Panel without an onToggle handler prop.
This will render a read-only field. If the field should be mutable use defaultExpanded. Otherwise, set onToggle.

3. Warning: Failed prop type: Invalid prop 'reaction' of type 'Object' supplied to 'ReactionTable',
expected instance of 'Reaction'.
    in ReactionTable (created by ReactionInfo)
also: ReactionRinChiKey, ReactionProperties, ReactionTlc

4. Remove unused variables

search review list

show lastest sample svg

show sample svg file in the publication list

add url on doi report

publishing message

Pubchem with no cid

check if cid null

Style improvement and published date on howto and news

1. add Published_At; default value is Created_At
2. the list is order by Published_At
3. set image style in quilleditor as 50vw
4. styling to fit small device

add counter in collection

repo-add-new-analysis-publication-fix

fix pubchem metadata doi

fix repo search issue

readonly when reaction published

Add Reviewed Collection

select reference when sample or reaction publish

repo search fix

Use Exact mass instead of Mass

refresh list after clicking review or accept

fix warning: typo class/className

sort analyses by extended_metadata.index

push state and routing cleanup

use aviator push state: absolute path no anchor
clean anchor on /mydb and /home path
redirecting on authenticate

mydb repo logo url

fix howto and newsroom path

disable reaction delete button when published

is_publish check fix

Submit with embargo

Submitter can put an embargo on his/her Sample/Reaction when he/she submits
for publication.

A new menu item named 'Embargoed Publications' is added on the menu.

A new collection named 'Embargoed Publications' is added on the collection
if user has put embargo on.

Submitter can generate a temporary account by clicking on 'Anonymous acct.',
and he/she will get the email with account and password from system.

Submitter can release an embargo only when all elements of this embargoed
collection are in state accepted.

Once the embarged is released, the related anonymous accounts will become invaild.

fix about page link

add skip_confirmation! when creating account

add alert and notification

display only when temperature is given

Display completed content of an analysis

Includes:
1. Remove the word 'Type' and 'Content'.
2. Display all of the content of an analysis.

This change is applied for: Publications page, Review page, Embargoed Publications page.

Stay on submission modal and download doi

Keep modal showed after clicking 'Reserve DOIs'
One new button behinds 'Reserved DOIs' for downloading DOIs in csv file format.

fix post processing embargo release

Not recognize activeKey prop warning on review and embargoed page

Warning: React does not recognize the 'activeKey' prop on a DOM element. If
         you intentionally want it to appear in the DOM as a custom
         attribute, spell it as lowercase 'activekey' instead. If you
         accidentally passed it from a parent component, remove it from the
         DOM element.

It is related to Nav and Navbar/NavbarForm. Remove and add css for styling.

publication decline and submitter comments

add page contactÄ

fix mail_reviewed_request

delete embargo function

clean js warning, refer to #215 for the details

Add Embargo description

fitler product which has no doi

Analyses in review and mydb view have same sequence

1. Sorting analyses in Review and Embargo page before rendering Analyses information
2. Remove console.log
3. Replace 'dark' with 'default' to eliminate js warning

decline button title

fix the currentElement null issue

repository license link

fix upload issue with .basename and add few css for UI

Metadata preview and download

A new feature Metadata on Review Page, user can preview/download
Metadata which send to Datacite in one zip file.

Refer to https://git.scc.kit.edu/ComPlat/chemotion_REPO/issues/223
for details.

process remove from all collections review

add metadata download button on publication page

Get first few lines, e.g. 6 lines, as sub-description

state changed before job called

Styling on How-To

We make some updates based on the feedback from Nicole. Please refer to
https://git.scc.kit.edu/ComPlat/chemotion_REPO/issues/230.

Besides,
Use cache: no-store to see if it works for the file cache issue.

howto and news now public

job to get SID by DOI

icon to link pubchem sid

clean db/migrate

fx

howto rm labels

scrollbar adjustment

Statistics info

Add total number of Samples, total number of Reactions, and
(the top 3) total number of Analyses on Welcome page.

reaction-submissions-mandatory-check

w

disable publish button when sample is unsaved

OLS for doi

update Gemfile.lock

fix reaction product doi display issue

advanced search by author for sample

sorting by published at

analysis-type-join-with-synonym

use trim to removes all the whitespace characters (space, tab, no-break space, etc.) and all the line terminator characters (LF, CR, etc.)

upd schema

advanced search by ontologies

Submissions mandatory check for re-submit

Apply submission checks when user re-submit reaction or sample. We still
perform these checks in front-end (not as title described).

When publish a sample, molecule(sample) check will be performed.

When user publish a reaction, both reaction check and molecule(sample) check
will be performed in one go.

If user publish a sample which is associated with a reaction, the system
will pop-up a message with reaction link so user can go to reaction to publish.

advanced search prevent sql injection

embargo pubchem

cap deploy: link public/ontologies dir

Creative Common License

Add 'Choose license' with CC0, CC BY and CC BY-SA options on user
submission; use CC BY-SA as default value.

Remove 'Creative Common License' relateds from page bottom.

Based on Datacite metadata schema 4.1 (which is used by chemotion_REPO),
this license data will be part of metadata_xml with tag <rights>
(under <rightsList>) and we will use the title/description from
Creative Common, which are
- Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) for CC BY-SA
- Attribution 4.0 International (CC BY 4.0) for CC BY
- CC0 1.0 Universal for CC0

Three SVGs(CC BY-SA, CC BY, CC0) from Creative Common
are added to public/images/creative_common.

show state accepted to review page

fix solvent calculation

fix solvent

submission be analyses type check

Check if kind value is with |

User registration: enable organisation input

Use Directive: upd txt for commercial use

directive in public html file

- render partial from public/directives/diretives.html for new
registration page
- react parse html for directive tab page

- content:
 -- add email for retraction
 -- precise cookie info
 -- adapt for commercial use license

directives content: fix html reserved charactes and other typos

directives: add list of available licenses

Add related identifier for reaction analyses and product

Add reaction analyses DOIs into relatedIdentifiers of datacite reaction xml, with relationType is 'HasPart'.
Add reaction DOI into relatedIdentifiers of datacite sample xml, with relationType is 'IsPartOf'.

Plus:
Encode 'description' of datacite reaction xml.

Consent of license

Add Legal Code link for user to view the license legal code.
Two checkboxes are added for CC0 license to get user's consent.

fix affiliation sorting and review display

A public api to get published molecule id, reference: https://git.scc.kit.edu/ComPlat/chemotion_ELN/issues/794

fix no action connected when user click How-To Editor in the dropdown

add delete doi api on datacite

Display authors information on published dataset page

Add 'Published On', 'Authors' and affiliation information on dataset page.

Select Coauthors lists ELN confirmed accounts

Only confirmed accounts are listed in Select Coauthors; filter out coauthors
with confirmed_at is nil when processing publish procedure.

remove affiliation group code

Submission check on co-author data

Check if co-author is valid or not; if co-author is invalid,
user will get the error message and the submission will stop.

exclude 103 on sync collection label

upd Gemfile.lock

rm env data

upd README for repo

non-published-reaction-goes-to-list-view

show short_label on review list

fix publication search alignment and add space on author name

Show under review and under embargo statics

About page: upd licensing txt

highligt current selected element in the list - publication, review, and embargo

bug fix on review page when reviewing element has analysis without type

use editor blocks instead of only one quilleditor

pid routing

TOS update

sid job with completed only

generate doi when structure changed and accept

TOS upd

reviewer comments save WIP

Independent scroll bar in review comment panel

When user clicks on 'Reviewer comment' of MyDB, the system displays MyDB data
and submission data in one screen for user to view detail data and comments
from the reviewer at the same time.
Add scroll bar for MyDB data and submission data so user can inspect the data
by scrolling the document separately.

Additional: use 'pre-wrap' for summary comment.

repo review button bugfix

add chemspectra deploy config

fix review with comments on details

embargo to remove pending tag

pubchem_V2000 T9 filter

Export collections for mydata and elngate only

Only 'My Data' collection and 'ELN Gate' collection are used in
Repository. Therefore, remove other collections(incl. 'All') from
'Export collections' UI.

Disable 'Import collections' from menu due to the current logic of
ELN 'Import collections' function is not suitable for Repository.

sort published reaction by published date

chr id

Search reaction function

Add search function on Publications page when switch type is Reaction.
Additional:
1. Set default value in case the user has no layout data.
2. Rebuild pg_search by using rake with 'rake pg_search:multisearch:rebuild[Reaction]' or
in the console with 'PgSearch::Multisearch.rebuild(Reaction)' or 'PgSearch::Multisearch.rebuild(Reaction, false)'.

Add features on Welcome page

change from ChRx to CRx

add reviewer and public collection to env setting

npm: svg-zoom downgrade back to 0.1.5

typo uniq ChemRep id

rename chemspectra

new editor for newsroom

make the reactions visible per default (instead of molecules)

REPO copy to clipboard analysis desc

Revert "Resolve "report-fetch-with-buffer""

This reverts commit 51ce7aa.

Report: [1] fetch list by difference [2] fix load sync & share elements

Update ITG to IBCS

About page:
- change 'Institute of Toxicology and Genetics (ITG)' to 'Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS)'
- change 'Institute of Toxicology and Genetics' to 'Institute of Biological and Chemical Systems – Functional Molecular Systems'

Contact page:
- change 'Institute of Toxicology and Genetics (ITG)' to 'Institute of Biological and Chemical Systems – Functional Molecular Systems (IBCS-FMS)'

Additional change: code linting

News room for the chemotion.net page

Refer to https://git.scc.kit.edu/ComPlat/Zettelkasten/issues/43
Modification:
1. Add 'Newsroom' link on the main page.
2. Clean code

Duration of reaction is mandatory for submission

Add validation on Duration of reaction. Duration is mandatory for submission.
Note: For re-submit/publish case, the validation of Duration is already existed.

Indicate the mandatory fields for publication

Add 'RequiredLabel' as a common component to indicate mandatory fields for submission.

review page with filter set to pending by default

13C counting: count missing signal statement

wip, yield

wip

switch switch to tabs

disable scheme-only reaction publication

publishing concern: clean

WIP revamp review job

fix method naming when oub declined

mv collection logic to pub model

use state constant

WIP refactor reviewing job move logic to model

refactor declined thru element deletion

DRY repo_api by moving logic to publication model

lint

tmp fix to not email some reviewers

lint

WIP DRY

Quillviewer not to remove formating

atom count in analysis NMR description
allow decimal count
fix  H nested bracket count

add scheme only on public view, env variables, and lint

scheme only BE

fix reject samples

check if regenerate doi is needed

disable reserved DOI

pagination for review page

f

Reaction product doi display incorrect

Use taggable_data

scheme only yield and author

DRY for sample/reaction details of repository

Common:
1. split MetadataModal, ReviewModal, CommentModal, CommentBtn into files

Reaction:

1. add RepoReactionDetails.js
2. replace the codes for rendering reaction details with RepoReactionDetails.js
- RepoReviewDetails.js
- RepoEmbargoDetails.js
- RepoElementDetails.js
- ReactionDetails.js
- ReactionDetailsRepoComment.js

Sample:

1. add RepoSampleDetails.js, RepoSample.js
1. replace the codes for rendering sample details with RepoSampleDetails.js
- RepoReviewDetails.js
- RepoEmbargoDetails.js
- RepoElementDetails.js
- SampleDetailsRepoComment.js

Features:
1. User can leave the comment on ELN view now
2. User can only close the modal by clicking on Close button or the Close icon (x) on the right-top

Bug-fixes:
1. Click Dataset link and get blank page
2. Get blank page on Review when switch from Publications and currentElement exists
3. Align labels on Publications view

Link to mydb missing on review panel

Add codes to identify enabled/disabled MyDB link from different response structure.

Align content of analysis on view page

Add style to align the analysis content with ID element.

show fulldoi on review

move embargo to another embargo bundle

All validated analyses selected by default

The validated analysis is checked/selected(publish=true) by default.
If users uncheck/unselect the analysis, then this analysis will not
be checked/selected automatically in the future even it is validated.

reaction publish duration

show contributor as published by as priority

correct script error

upd db/schema

fix reaction duration set value

scheme only doilink and description and properties

Page margin of element detail

Use the scroll of panel when element detail is basic view (not full screen)

f

Add codes to identify enabled/disabled MyDB link from different response structure.

hidden search input by default

MyDB case

show user define iupac name on publication

public view search tool: fix suggestion and search

TODO check suggestion/search on schemOnly

Style search input of publications

1. reset search input of StructureEditor
2. align elements

Eager loading detected on clicking mydb

Refer to https://git.scc.kit.edu/ComPlat/chemotion_REPO/-/merge_requests/292
Use .joins to get the count of Sample and Reaction

change published analyses from Serializer to Entity

publication preview image fix

Missing reaction description on publications

1. Show 'Description' and 'Additional information' if there is any.
2. Set defaultExpanded of 'Reaction Table' as false.
3. Wording, please refer to https://git.scc.kit.edu/ComPlat/Zettelkasten/issues/65
4. Put Formula/IUPAC on a new line if any
5. Add DOI copy function on the elements of Review page

modify publication validation message

fix withdraw issue when original element is deleted

doi copy function by default

1. add doi copy function to Product and it analyses on Review and Embargo page
2. set defaultExpanded of RInchiKey panel as false, of Reaction Table panel as true

Blank page after resubmit reaction with new added product

Add logic to handle user re-submit with new added product case.

disable mailing to reviewer

upgrade to schema 4.3

disable-jcamp-process-when-element-submit

disable sending mail to reviewers

REPO FACTOR

Update chem_scanner gem, text in table is not used while splitting

Update chem_scanner gem, treat charge independently with fragment

Skip if there is any error while processing CDX

Update new version of chem_scanner gem

Use backend ketcher for Chemscanner

 Conflicts:
	package-lock.json

Configurize ketcher URL

show published scheme only reaction literature in ELN view

deploy config upd

fix deploy config for ketchBE

Style search and smile of publications page

1. apply harsh edge to search
2. fix border and overlap
3. fix smile data goes beyond the tabs

add help infomation on tabs of publications

incorrect-substructure-search-data-display-on-publication

rearrange statistic layout

readable statistic info when resize browser window

new intro style

search by chemotion-id

Yield validation of submission

If the yield is not given in the publishing panel, there should be a
warning and the submission only allowed if the yield is given.

For multiple products case, at least one should be non zero.

This applies for both reaction and scheme-only reaction.

Note: scheme-only reaction can only be rejected or accepted;
Therefore, re-submit is not applicable to scheme-only.

add element_type on suggestion

review history

Save collapse settings

Add ArchivedManagement view: manage archived/actived files

Update product name while importing

Chemscanner importing run as a delayed job

Delete descendant source if parent is deleted

Use rdkit for SVG composer for chem_scanner, update chemscanner_composer

review history column history fix

review-column-history-info-collapse

new style for 'no preview available' case

enable prediction function for view user

repo review search

activate Anonymous account by default

activejob_dj_overrides

User comments

fix publishing job retry

Set as default to use description field

For 'scheme-only', set 'add the description field?' as checked by default

fix block syntax

Analysis preview thumb and image no match

Issue:
On publications page, user clicks on the preview image of analysis and gets thumb file in pop modal. (w/o login)
On publications page, user clicks on the preview image of analysis and gets a different image in pop modal. (w/ login)

Fix:
1. When user re-submits with new attachments, these attachments should be copied to publications folder
2. Refactor the preview_image: add id and filename as return value

Additional:
1. DRY with previewContainerImage
2. Remove unused codes

Contributor information

Add an information for the scheme only submissions at the publication page assigned to the 'Contributor'.

User comments for sample and reaction

null analyses affiliation

export doi info

fix repo reaction container issue

info button for table, description and additional information... field

Add info for 'scheme', 'description' and 'additional information...' fields of Reaction.
Display info while hovering the text for required fields; set font color as red to mark it as required field

info text upd

show/hide help-button and linting

fix repo search bug

correct email

change to the right type

xvial input and display

add compound link

update per feedback from https://git.scc.kit.edu/ComPlat/chemotion_REPO/-/merge_requests/333#note_191189

UI control and improvement on xvial

Per request,
- the registered sentence only appears in the cases where an X-Vial number is entered
- the X-Vial number is not visible to all users
- add the email address of the requesting user to the mail; send the request email to compound team and send the confirmation email to the requester
- add to the information button about Youtube channel and our how-to pages

Remind user to log in to send request

Secret external label

The external label of sample is not visible for all users (except the reviewer and
the owner himeself/herself) if the sample is published. This also applies for
the case when user chooses to 'Show sample external name on title'.

Add DOI in SI report

there is a case that collection_label of reactant is empty

fixed no response on substructure search

remove review history from published element

eliminate js warning

element-tag-doi-for-reviewing-elements

element-remove-from-contributor-pending-collection-after-release

send-email-when-pubchem-timeout

no-process-embargo-rejected-sample

fix process element

move collection before deletion

doi doc report: rm unnecessary whitespace

delete elements fix

use DOI in report supporting-information-standard-reaction

Product X-Vial

1. Add X-Vial function on product
2. Add info button on X-Vial button
3. Remove X-Vial information from published reaction list

add xvial to public reaction list

disable instrument tex for publication and visible for reviewing

increase author list to 10

eliminate js warning

Analysis view button on public page

Add viewing spectra function on analysis of public samples, and reaction product as well.

enlarge image when hovering, and zoom function on svg of detail

lizenz text gestaltung

1. text adjustment per request
2. add 'No License' option; when user chooses 'No License', there will be
no license icon or wording shown on the page and the no rights data
sent to dataCite.

add animation on MyDB link

my collaboration WIP

service

collaborator-current-affiliations
- Fetch data from a collection(Repo: Open Data Collection) of Compound platform.
- Use compound_open_data.yml as configuration file, put aurthized user id in allowed_uids.
Dependabot couldn't find the original pull request head commit, 445e993.
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](puma/puma@v5.6.7...v5.6.8)

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

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [webpack-dev-middleware](https://github.com/webpack/webpack-dev-middleware) from 5.3.1 to 5.3.4.
- [Release notes](https://github.com/webpack/webpack-dev-middleware/releases)
- [Changelog](https://github.com/webpack/webpack-dev-middleware/blob/v5.3.4/CHANGELOG.md)
- [Commits](webpack/webpack-dev-middleware@v5.3.1...v5.3.4)

---
updated-dependencies:
- dependency-name: webpack-dev-middleware
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Bumps [tar](https://github.com/isaacs/node-tar) from 6.1.11 to 6.2.1.
- [Release notes](https://github.com/isaacs/node-tar/releases)
- [Changelog](https://github.com/isaacs/node-tar/blob/main/CHANGELOG.md)
- [Commits](isaacs/node-tar@v6.1.11...v6.2.1)

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

Signed-off-by: dependabot[bot] <[email protected]>
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