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chore: Bump tar from 6.1.11 to 6.2.1 #95

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959fbbe
download analysis of publication without sign in
cllde8 Mar 24, 2021
f960b97
view sprectra of products
phuang26 Mar 29, 2021
78bb8cd
orig. is not required
cllde8 Mar 29, 2021
654515d
export embargo collections
phuang26 Mar 31, 2021
58881df
display 0 as empty
cllde8 Apr 1, 2021
c18112a
search embargo bundle number
phuang26 Apr 7, 2021
fa6f6ce
display name on review page
cllde8 Apr 12, 2021
3323bc5
embargo in reaction list
phuang26 Apr 8, 2021
27d7841
search by authors or contributors
phuang26 Dec 3, 2020
5eb2c49
sanitize_sql
phuang26 Apr 15, 2021
a63b2ee
allow users to edit spectra's content
Apr 7, 2021
14ad605
deploy config mod
PiTrem May 14, 2021
95af2e7
add xvial symlink
cllde8 May 14, 2021
c446392
minor upd Gem.lock db/schema
PiTrem May 15, 2021
7ba3d51
add default profile
PiTrem May 15, 2021
dd8d587
FE fix after rebase
PiTrem May 15, 2021
8aae173
update style back to original setting
cllde8 Jun 23, 2021
bbd9250
use 'mass spectrometry' and 'IR'
cllde8 Jun 23, 2021
2aa2489
publication embargo search
phuang26 Jul 14, 2021
0c65bd3
make regenerate button for all unoriginal jdx files
Jun 7, 2021
99b6bae
regenerate for reviewer only
phuang26 Jul 19, 2021
90cf380
check and fix
phuang26 Aug 4, 2021
8bd3b06
smiles to SMILES
phuang26 Aug 4, 2021
ba10339
add permission on repository_api reaction and sample
phuang26 Aug 4, 2021
4733cdb
add validation
cllde8 Aug 5, 2021
24b9315
fix migration file for solvent
phuang26 Aug 6, 2021
3fe0bc4
review reaction scheme
phuang26 Sep 29, 2021
a1ee48b
fix duplicate function name from ELN rebase; publish reaction
cllde8 Oct 5, 2021
56ac860
styling
cllde8 Oct 14, 2021
a758c2a
reaction list style
phuang26 Oct 21, 2021
9dffd12
focus on style of review page
cllde8 Oct 22, 2021
eaf1f8a
publication molecule layout
phuang26 Nov 13, 2021
84d4534
add publish date to new layouts
cllde8 Nov 17, 2021
bfb1996
change style to solve overlap issue
cllde8 Nov 18, 2021
17776bc
directing to the sample of publication
cllde8 Dec 8, 2021
8691691
fix e.split on review page issue
cllde8 Dec 9, 2021
c607450
fix e.split on review page issue
cllde8 Dec 9, 2021
bccefa8
review submitter list issue
phuang26 Jan 13, 2022
8d0abd6
publication author and the link
phuang26 Jan 11, 2022
74cdd7c
1. unify the terminology: use Reference(s)
cllde8 Jan 4, 2022
5df9ca9
move js file to packs
phuang26 Feb 9, 2022
5553061
migration file
phuang26 Feb 24, 2022
625bd93
rm chemscanner
phuang26 Feb 24, 2022
a197ee8
chemscanner
phuang26 Feb 24, 2022
f00d154
submission validation and collection
phuang26 Mar 19, 2022
f8d2619
reference desc
phuang26 Mar 19, 2022
5336c12
rm dup. decoupled
phuang26 Apr 7, 2022
2789d46
ref
phuang26 Apr 7, 2022
f6e02fa
spectra 0.10.14-beta.0
phuang26 Apr 25, 2022
c36f3ca
Collection DOI
phuang26 Mar 30, 2022
36e3eed
Collection DOI
phuang26 May 16, 2022
ef18f79
Resolve "upgrade datacite schema"
cllde8 May 31, 2022
311ff69
nmrshiftdb solvent
phuang26 Jun 24, 2022
b94b3c6
add 'copy to clipboard' on collection doi
cllde8 Jun 29, 2022
809a36b
assign to embargo
phuang26 Jul 10, 2022
1fe8fa5
Resolve "publish when segment exist"
cllde8 Jul 13, 2022
471ce28
default segment of reaction, segment for publication
cllde8 Jul 14, 2022
f8ce8a1
att permission for seg
phuang26 Jul 14, 2022
38d693b
oai metadata
phuang26 Jul 19, 2022
dcfef11
submission date
phuang26 Jul 19, 2022
369af52
update
phuang26 Jul 19, 2022
0c4f50f
wip
cllde8 Jul 25, 2022
1107458
option to skip yield validation
cllde8 Aug 1, 2022
ec17981
how-to link and quill-viewer styling
cllde8 Aug 31, 2022
905dbb6
1. add a button to copy collection DOI
cllde8 Aug 31, 2022
6b95aba
review comment
phuang26 Oct 20, 2022
b5aee6f
the focus is on the selected record in the list when redirecting from…
cllde8 Oct 26, 2022
261d98c
switch tab after searching by inchi
cllde8 Oct 27, 2022
089060f
review comment r
phuang26 Oct 27, 2022
1ca83cc
added molecule archive
cllde8 Oct 19, 2022
3cf66e2
add xvial filter
cllde8 Oct 28, 2022
4f2681a
add xdata to the list
cllde8 Nov 4, 2022
3bddad9
count of compound
cllde8 Nov 16, 2022
8e1b733
publication element index
phuang26 Nov 17, 2022
a5c80de
import collection
phuang26 Nov 18, 2022
5f5bd19
embargo author
phuang26 Nov 30, 2022
9ed4e19
new content of project description of about
cllde8 Jan 4, 2023
4b84863
update copyright statement
cllde8 Jan 5, 2023
44f01fb
linting
cllde8 Jan 9, 2023
b1f8894
landing page updates:
cllde8 Jan 4, 2023
5f26960
rename terms of service to directive
phuang26 Jan 2, 2023
cfacf00
fix dataset doi cannot be resolved issue
cllde8 Feb 2, 2023
1711436
add embargo link on review and copy function
cllde8 Feb 2, 2023
417e8e5
fix routing
cllde8 Feb 7, 2023
ece9e74
fix collection routing and info modal
cllde8 Feb 7, 2023
82e35cb
fix based on feedback
cllde8 Feb 7, 2023
19d55a1
workaround for react-svg-file-zoom-pan-latest library issue
cllde8 Feb 7, 2023
faf5f3f
chem converter
phuang26 Feb 8, 2023
ed58629
fixed: redirect to the latest published element successfully, but no …
cllde8 Feb 12, 2023
54cb453
review comment fix
phuang26 Feb 14, 2023
f6b0c37
hide info when inchikey is dummy
cllde8 Feb 15, 2023
e0fd782
embargo btns
phuang26 Feb 16, 2023
d8c7bde
Update Navigation.js
PiTrem Feb 20, 2023
cf584dd
converter for user
phuang26 Feb 17, 2023
8775c7a
converter config file
phuang26 Feb 23, 2023
d230806
embargo email issue
phuang26 Mar 2, 2023
a89a20b
upgrade chemspectra
phuang26 Mar 2, 2023
e5d7884
Resolve "porting the 3d viewer"
cllde8 Mar 6, 2023
c2c3753
Revert "Merge branch '520-upgrade-chemspectra' into 'server_chemotion…
phuang26 Mar 6, 2023
4c65586
upgrade chemspectra
phuang26 Mar 2, 2023
cbff938
embargo job fix
phuang26 Mar 6, 2023
3af15b8
disable 3d molecule
phuang26 Mar 6, 2023
1d4a2eb
publication page issue
phuang26 Mar 6, 2023
5aa6845
review bugfix
phuang26 Mar 17, 2023
4f77dee
fix file ext issue
phuang26 Mar 22, 2023
96c187e
resourceTypeGeneral sample
phuang26 Mar 22, 2023
8810e06
add example text on request form
cllde8 Mar 30, 2023
85c196c
increase font size
cllde8 Apr 2, 2023
66a3ca6
fix how to
phuang26 Apr 4, 2023
8e6ba08
ketcher backend
phuang26 Apr 14, 2023
07e0ac8
metadata description of sample publication
cllde8 Apr 6, 2023
a8469ee
sample representation on landing page
cllde8 May 4, 2023
046dc2a
shibboleth and group leader review
phuang26 Apr 12, 2023
8bd9dbb
Resolve "molecular mass descriptor in sample metadata"
cllde8 May 8, 2023
b3edbae
review notification
phuang26 May 8, 2023
d94fe35
group default value
cllde8 May 9, 2023
254040b
rm review notification
phuang26 May 9, 2023
fc17667
fix White Screen when clicking on Analysis DOI
cllde8 May 10, 2023
bd0d7c3
fix white page while doi is null
cllde8 May 10, 2023
da43e36
fix the incorrect license icon usage
cllde8 May 10, 2023
307f8fd
msg fix
phuang26 May 12, 2023
727188e
user reivew and svg fix
phuang26 May 16, 2023
37e6ca0
remove log
phuang26 May 16, 2023
e2d8392
group lead review update
phuang26 May 19, 2023
322e5a4
increase font size and add space
cllde8 May 23, 2023
6f855a8
add comp-number to published sample page
cllde8 May 23, 2023
b10e35f
Resolve "review ui reload issue"
phuang26 May 23, 2023
0ba35b1
Resolve "compounds visibility"
cllde8 May 24, 2023
70cde4f
anchor on publication page
cllde8 May 24, 2023
27853b6
add solvent to sample metadata
cllde8 May 24, 2023
8ca56fe
published year
phuang26 May 24, 2023
673e9cc
linked-data
phuang26 May 24, 2023
453ebbb
add original id to compound list
cllde8 May 26, 2023
fe34ca8
linked data api
phuang26 Jun 2, 2023
001eea4
gate transfer
phuang26 Aug 5, 2022
fdc0c07
revise readme file
cllde8 Jun 16, 2023
5099d45
use ISO date format for publication data
cllde8 Jun 16, 2023
edd9457
correct the date format at back end
cllde8 Jun 19, 2023
e716d31
lock element after submit
cllde8 Jun 25, 2023
4032eca
Resolve "physical properties"
cllde8 Jun 27, 2023
d7aefcb
set license to CC BY as default
cllde8 Jun 26, 2023
cc591b4
creation date of import
phuang26 Jun 26, 2023
1b19e20
fixed blank page issue on molecule archive after searching
cllde8 Jun 6, 2023
b704349
introduce linked data component
cllde8 Jun 27, 2023
5bd1310
add info to lock element function
cllde8 Jun 27, 2023
afd939f
expand dataCatalog schema
NRayya Jun 24, 2023
fbfe087
correct dataCatalog syntax error
cllde8 Jun 30, 2023
23c505e
fix data catalog syntax error and add styling
cllde8 Jun 30, 2023
cac3746
compounds for public
cllde8 Jul 3, 2023
dfde4aa
enable oo
phuang26 Jul 3, 2023
c5903e8
add license to linked data
phuang26 Jul 4, 2023
ad208ae
rm confirmsto
phuang26 Jul 5, 2023
4b82876
add logo
cllde8 Jul 11, 2023
805b6e9
Resolve "molecule viewer"
cllde8 Jul 16, 2023
56c964b
fixed the issue that different molecule shows the same in the viewer
cllde8 Jul 16, 2023
a78cb14
code simplification
cllde8 Jul 17, 2023
6fbaf4c
compare view gets blank page
cllde8 Jul 17, 2023
1b51641
fix chembox endpoint
cllde8 Jul 18, 2023
bca26e5
embargo accepted
cllde8 Jul 29, 2023
d372ed2
LabIMotion
cllde8 Jul 29, 2023
b3f8cb2
cap deploy
phuang26 Aug 1, 2023
4a310c4
add contact block on mydb page
cllde8 Aug 3, 2023
bddbd55
con state
phuang26 Aug 4, 2023
57449bb
fix the unit cannot display issue
cllde8 Aug 7, 2023
8a78c2e
upgrade review functionality
phuang26 Aug 13, 2023
8c3c2e8
labimotion hub list
phuang26 Aug 17, 2023
9eb3730
Resolve "designer versioning"
phuang26 Aug 29, 2023
d22ba93
add fetchKlass
phuang26 Aug 29, 2023
4deeffb
table select of viewer
cllde8 Aug 30, 2023
dce5bbc
move klasses.json
phuang26 Aug 30, 2023
5459600
new comment for grouplead
phuang26 Aug 30, 2023
f021b7e
Resolve "add nfdi4chem award"
cllde8 Sep 1, 2023
1e5b86f
Resolve "global user label"
phuang26 Sep 1, 2023
9662585
copy element segments check
phuang26 Sep 1, 2023
21e2abf
spectra duplicate issue
phuang26 Sep 1, 2023
0e603a0
define unit is not working
cllde8 Sep 4, 2023
f69c8d8
Resolve "make properties invisible"
cllde8 Sep 5, 2023
554d3c6
leave a comment function
cllde8 Sep 5, 2023
2f0b31e
Resolve "make properties invisible on publication page"
cllde8 Sep 17, 2023
6b735b3
Resolve "generic dataset of publication page"
cllde8 Oct 19, 2023
c8c50a5
fix the issue that occurs when there is no file extension in the file…
cllde8 Oct 19, 2023
0122e3b
Resolve "reviewers introduction"
cllde8 Oct 24, 2023
663d9cb
fix the unique key of child issue
cllde8 Oct 24, 2023
0f9b899
Resolve "option to add all samples"
phuang26 Oct 24, 2023
6c5cd79
suggestion for labimotion
cllde8 Oct 25, 2023
9ed2a9f
params for JSON-LD
phuang26 Oct 27, 2023
b5e7d50
update review guidelines
cllde8 Oct 29, 2023
20fb199
review embargo list
cllde8 Nov 2, 2023
61ba626
upgrade nmrium
phuang26 Nov 7, 2023
f80d042
fix the invalid date format issue
cllde8 Nov 7, 2023
065584c
Resolve "search tool on publication page"
cllde8 Nov 7, 2023
6db5ff3
Resolve "new 3d for cif"
cllde8 Dec 1, 2023
4981bf1
do not show the image for publications where no preview available
cllde8 Jan 3, 2024
3d120e4
analysis definedTerms
phuang26 Jan 3, 2024
61fd144
upgrade lib
cllde8 Jan 3, 2024
ab8617d
feat: report peaks from XRD (#1614)
f-idiris Nov 14, 2023
ee4d105
feat(spectra): update chemspectra backend to read some jcamp v6 (#1603)
baolanlequang Nov 14, 2023
ecccbd0
feat: display mail collector address as info in the Inbox (#1529)
PiTrem Nov 16, 2023
cf1e61a
feat: drag samples and elements to segment (#1623)
phuang26 Nov 16, 2023
735b42d
feat: include chemicals with import and export of collections (#1604)
adambasha0 Nov 16, 2023
3a4390e
fix: the attachment to be removed from the inbox when assigned to a s…
TasnimMehzabin Nov 17, 2023
ca8f275
feat: upgrade-converter-to-v1.1.1
phuang26 Nov 20, 2023
fec6da4
fix(spectra): remove blank line when saving peak
baolanlequang Nov 20, 2023
1e046ee
fix(spectra): Add/remove multiplicity peak buttons(#1630)
baolanlequang Nov 20, 2023
a14292c
chore: Bump rmagick from 5.0.0 to 5.3.0
dependabot[bot] Nov 20, 2023
1a7feba
fix: allow import of molecule_name on sample import for xslx format
adambasha0 Nov 20, 2023
8bc37ce
chore: upd node engine for dev container (#1635)
PiTrem Nov 21, 2023
56c6d4c
feat: Changed Mail collector rules
StarmanMartin Nov 21, 2023
b6072da
feat: add volume field in inventory tab (#1613)
adambasha0 Nov 24, 2023
8c55f62
fix: collection management right click on the add button to not drag …
FabianMauz Nov 29, 2023
969d826
fix: update chemspectra client to prevent crash on CV layout
baolanlequang Nov 29, 2023
3da928a
feat: show research plan links in reaction (#1575)
mehreenmansur Nov 29, 2023
4dd79cc
fix: reaction sort column value not being persistent for updated_at c…
TasnimMehzabin Nov 29, 2023
5ca9d27
fix(spectra): correctly trigger action spinner when saving peaks to a…
baolanlequang Dec 5, 2023
9d68f45
fix(spectra): order of J value
baolanlequang Dec 5, 2023
64cb703
feat: sorting option for datasets and attachments in the inbox by cre…
TasnimMehzabin Dec 5, 2023
f74ac62
test: fix test with deviceBox sorting in inbox
TasnimMehzabin Dec 7, 2023
1094874
feat: add the option to change the inbox sizing
TasnimMehzabin Dec 12, 2023
212838a
fix: si-spectra report generation to work even without preview
mehreenmansur Dec 12, 2023
b5f4b41
fix(UX): molecule title layout and element table header responsiveness
mekkyz Dec 12, 2023
3e28769
chore: Improve Dev Setup by autorecognizing the installed tool versio…
jhmegorei Dec 13, 2023
4b7229a
fix(spectra): react-spectra-editor upd to correct molecule display wi…
baolanlequang Dec 20, 2023
9891afd
feat: add chemspectra with ref peaks (#1596)
baolanlequang Dec 20, 2023
5ca9277
fix: camelcasing attributes for proper display of SVGs
PiTrem Dec 20, 2023
c3145b3
fix: remove original data from nmrium data before storing it
baolanlequang Dec 20, 2023
960e810
feat: Unified attachment list
mekkyz Dec 20, 2023
88062a8
fix: attached research_plans in screens not being imported from colle…
TasnimMehzabin Dec 21, 2023
df45111
chore: bug fixes after rebase
cllde8 Jan 4, 2024
f9e9bcb
Extending chemotion_ELN with Repository functions
Sep 27, 2017
6cbc6fb
Repo update (#45)
phuang26 Jun 7, 2023
da11a39
Update README.md
phuang26 Jun 7, 2023
1b8546f
remove unused code
phuang26 Jun 12, 2023
ec0a015
REPO FACTOR
Sep 27, 2017
e5b9a5d
edit authors function before release
phuang26 Oct 19, 2020
af909f4
rubocop and add isSubmitter instead of isReviewer
phuang26 Oct 23, 2020
99b7a58
Collection description on hovering
cllde8 Nov 4, 2020
367b8e2
Provide a X-Vial list in Chemotion Repository for the authorized users.
cllde8 Nov 3, 2020
75157e1
add xvial and type check
cllde8 Nov 20, 2020
0c59147
download analysis of publication without sign in
cllde8 Mar 24, 2021
021024d
view sprectra of products
phuang26 Mar 29, 2021
5fd2d12
minor upd Gem.lock db/schema
PiTrem May 15, 2021
ac68a80
publication embargo search
phuang26 Jul 14, 2021
ee0d80b
Chemotion Repository 2.0.0
cllde8 Jan 16, 2024
c0cdea4
chore: Bump follow-redirects from 1.14.9 to 1.15.5
dependabot[bot] Jan 16, 2024
9d58f39
chore: Bump puma from 5.6.7 to 5.6.8
dependabot[bot] Jan 16, 2024
12220c3
chore: semver vulnerable
cllde8 Jan 18, 2024
d0b9b97
chore: upgrade lodash 4.17.21
cllde8 Jan 18, 2024
ff47154
chore: github ci
cllde8 Jan 18, 2024
b4f7a4a
chore: Bump webpack-dev-middleware from 5.3.1 to 5.3.4
dependabot[bot] Mar 23, 2024
0ecd435
chore: Bump tar from 6.1.11 to 6.2.1
dependabot[bot] Apr 11, 2024
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10 changes: 0 additions & 10 deletions .babelrc.bak

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1 change: 1 addition & 0 deletions .dockerignore
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@
backup
uploads
public
!/public/ontologies_default/
.gitignore
node_modules
tmp
Expand Down
16 changes: 0 additions & 16 deletions .env.dev.example

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40 changes: 0 additions & 40 deletions .env.development

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12 changes: 6 additions & 6 deletions .env.production.example
Original file line number Diff line number Diff line change
@@ -1,22 +1,22 @@
# default uri of your Chemotion ELN for http links in e-mails and notification:
PUBLIC_URL='http://sld.tld'
PUBLIC_URL='http://sld.tld'
# senders e-mail:
DEVISE_SENDER='[email protected]'
DEVISE_SENDER='[email protected]'

## SMTP config
## SMTP config
# Remote mail server
SMTP_ADDRESS='smtp.sld.tld'
SMTP_PORT=587
# login user name & password:
SMTP_USERNAME='[email protected]'
SMTP_USERNAME='[email protected]'
SMTP_PASSWORD='s3cr3tPW'
# optional, HELO domain
SMTP_DOMAIN='sld.tld'
# detect STARTTLS
SMTP_TLS=true
# authentication type ('plain' 'login' (Base64 encoded) or 'cram_md5')
SMTP_AUTH='plain'
# how OpenSSL checks the certificate ('none' or 'peer')
# how OpenSSL checks the certificate ('none' or 'peer')
SMTP_SSL_MODE='none'

# disable mail delivery
Expand Down Expand Up @@ -52,7 +52,7 @@ DEVISE_DISABLED_SIGN_UP=''
DEVISE_NEW_ACCOUNT_INACTIVE=false

# Application's title
APPLICATION_TITLE='Chemotion'
APPLICATION_TITLE='Chemotion Repository'

DATA_CITE_BASE_URI=https://api.test.datacite.org
DATA_CITE_PREFIX=prefix
Expand Down
31 changes: 0 additions & 31 deletions .env.test

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8 changes: 6 additions & 2 deletions .eslintrc
Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,17 @@
"parser": "@babel/eslint-parser",
"plugins": [
"react",
"no-relative-import-paths"
"no-relative-import-paths",
"prettier"
],
"env": {
"browser": true,
"node": true
},
"extends": [
"airbnb",
"prettier",
"plugin:prettier/recommended",
"plugin:react/recommended"
],
"rules": {
Expand All @@ -27,7 +30,8 @@
"code": 120,
"ignoreComments": true
}
]
],
"prettier/prettier": "error"
},
"settings": {
"import/resolver": {
Expand Down
46 changes: 0 additions & 46 deletions .github/ISSUE_TEMPLATE/bug_report.md

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19 changes: 0 additions & 19 deletions .github/ISSUE_TEMPLATE/enhancement.md

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18 changes: 0 additions & 18 deletions .github/ISSUE_TEMPLATE/feature.md

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15 changes: 0 additions & 15 deletions .github/ISSUE_TEMPLATE/greater-code.md

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39 changes: 0 additions & 39 deletions .github/ISSUE_TEMPLATE/installation-issue.md

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21 changes: 0 additions & 21 deletions .github/PULL_REQUEST_TEMPLATE/generic.md

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21 changes: 0 additions & 21 deletions .github/pull_request_template.md

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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ jobs:
run:
shell: bash

container: complat/chemotion_eln_runner:v1.8.0
container: complat/chemotion_eln_runner:main

services:
postgres:
Expand Down
10 changes: 10 additions & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -94,6 +94,10 @@
!/public/images/ghs/
!/public/images/creative_common/

/public/intro/*
!/public/intro/.keep
/public/jsmol/*
!/public/jsmol/.keep
/public/editors/*
!/public/editors/.keep
/public/favicon.ico
Expand All @@ -120,6 +124,12 @@
!/public/json/pictograms.json


/public/jsmol/*
!/public/jsmol/.keep

/public/jsmol/*
!/public/jsmol/.keep

/public/zip/*
!/public/zip/.keep

Expand Down
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