chore: Bump json-jwt from 1.16.1 to 1.16.6 #80
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update package using chem-spectra-client version 0.10.11 update version of chem-spectra-client
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.
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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]>
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OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting If you change your mind, just re-open this PR and I'll resolve any conflicts on it. |
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Bumps json-jwt from 1.16.1 to 1.16.6.
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fcc22b0v1.16.69c4d842reject blank JWE87cb8c8v1.16.50c2c1a0add base64 gem as dependency6391631unify coding style0d5a266v1.16.4676bcderun CI on ruby 3.3413848cv1.16.3e5eff66cache only when kid is found, even unless auto_detect mode. and pass options ...3acd910v1.16.2Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting
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