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Publication versions #57

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6ff54b6
Merge branch '511-link-collection-doi-to-embargo-page' into 'server_c…
phuang26 Feb 7, 2023
e2e7898
Merge branch '512-fix-the-bug-for-hyperlink-export' into 'server_chem…
phuang26 Feb 7, 2023
e6a141e
workaround for react-svg-file-zoom-pan-latest library issue
cllde8 Feb 7, 2023
0a43d52
Merge branch '514-svg-does-not-load-properly' into 'server_chemotion_…
phuang26 Feb 7, 2023
af8153f
chem converter
phuang26 Feb 8, 2023
04196b7
Merge branch '513-chem-converter' into 'server_chemotion_net-5'
phuang26 Feb 8, 2023
c9e700d
fixed: redirect to the latest published element successfully, but no …
cllde8 Feb 12, 2023
3a8c4cb
Merge branch '515-the-latest-published-element-is-not-shown' into 'se…
phuang26 Feb 13, 2023
c02680c
review comment fix
phuang26 Feb 14, 2023
24f2b3e
Merge branch '508-doi-and-comments' into 'server_chemotion_net-5'
phuang26 Feb 14, 2023
fbb6646
hide info when inchikey is dummy
cllde8 Feb 15, 2023
374d6af
Merge branch '516-update-publication-for-decoupled-sample' into 'serv…
phuang26 Feb 16, 2023
8b2f237
embargo btns
phuang26 Feb 16, 2023
065286f
hr to h
phuang26 Feb 16, 2023
9c2a0ae
Merge branch '517-product-w-no-name' into 'server_chemotion_net-5'
phuang26 Feb 16, 2023
97159be
Update Navigation.js
PiTrem Feb 20, 2023
52862ac
converter for user
phuang26 Feb 17, 2023
dd5c327
Merge branch '519-converter-for-user' into 'server_chemotion_net-5'
phuang26 Feb 23, 2023
04166d8
converter config file
phuang26 Feb 23, 2023
d66fefc
embargo email issue
phuang26 Mar 2, 2023
4fb86b0
upgrade chemspectra
phuang26 Mar 2, 2023
0d56470
fix duplicated img
phuang26 Mar 2, 2023
e329bfd
Merge branch '520-upgrade-chemspectra' into 'server_chemotion_net-5'
phuang26 Mar 3, 2023
ca55bcd
Resolve "porting the 3d viewer"
cllde8 Mar 6, 2023
5e591c2
Merge branch '518-porting-the-3d-viewer' into 'server_chemotion_net-5'
phuang26 Mar 6, 2023
bc4258b
Revert "Merge branch '520-upgrade-chemspectra' into 'server_chemotion…
phuang26 Mar 6, 2023
8e8424a
Merge branch 'revert-e329bfd6' into 'server_chemotion_net-5'
phuang26 Mar 6, 2023
e0cea6a
upgrade chemspectra
phuang26 Mar 2, 2023
c0a7a9c
fix duplicated img
phuang26 Mar 2, 2023
0e382f7
embargo job fix
phuang26 Mar 6, 2023
5b26a9b
disable 3d molecule
phuang26 Mar 6, 2023
0b76463
publication page issue
phuang26 Mar 6, 2023
99bb0b9
Merge branch '521-disable-3d-molecule' into 'server_chemotion_net-5'
phuang26 Mar 6, 2023
a37be82
Merge branch '522-publication-page-issue' into 'server_chemotion_net-5'
phuang26 Mar 6, 2023
4259eb2
review bugfix
phuang26 Mar 17, 2023
c0cdada
Merge branch '523-review-bug-fix' into 'server_chemotion_net-5'
phuang26 Mar 17, 2023
296a1e1
fix file ext issue
phuang26 Mar 22, 2023
6dc9df5
resourceTypeGeneral sample
phuang26 Mar 22, 2023
94bb3da
Merge branch '524-email-error-handling' into 'server_chemotion_net-5'
phuang26 Mar 22, 2023
f944cc5
add example text on request form
cllde8 Mar 30, 2023
0e25b6e
Merge branch '525-information-request-form' into 'server_chemotion_ne…
phuang26 Mar 30, 2023
6844bdb
increase font size
cllde8 Apr 2, 2023
cd425db
Merge branch '526-styling-request-form' into 'server_chemotion_net-5'
phuang26 Apr 2, 2023
c75483b
fix how to
phuang26 Apr 4, 2023
6e36c6e
Merge branch '530-fix-how-to' into 'server_chemotion_net-5'
phuang26 Apr 4, 2023
37f782e
ketcher backend
phuang26 Apr 14, 2023
8325927
Merge branch '532-ketcher-backend' into 'server_chemotion_net-5'
phuang26 Apr 16, 2023
4f43aaf
add nmrium aasm_state
PiTrem Apr 20, 2023
3327d87
Merge branch 'aq8848-server_chemotion_net-5-patch-56097' into 'server…
phuang26 Apr 21, 2023
f9403d5
metadata description of sample publication
cllde8 Apr 6, 2023
9e819ac
Merge branch '531-description-of-sample-publication' into 'server_che…
phuang26 Apr 27, 2023
a23315f
sample representation on landing page
cllde8 May 4, 2023
53717f1
Merge branch '533-sample-representation-on-landing-page' into 'server…
phuang26 May 4, 2023
0a190b4
wip
cllde8 May 4, 2023
7bbc544
wip
cllde8 May 4, 2023
a339a1b
shibboleth and group leader review
phuang26 Apr 12, 2023
8b0b780
Merge branch '529-shib' into 'server_chemotion_net-5'
phuang26 May 5, 2023
f84b5f7
wip
cllde8 May 5, 2023
df4234f
wip
cllde8 May 5, 2023
3970240
Merge branch '534-description-of-sample-publication' into 'server_che…
phuang26 May 5, 2023
7257426
Resolve "sync spectra"
phuang26 May 5, 2023
365216e
Merge branch '535-sync-spectra' into 'server_chemotion_net-5'
phuang26 May 5, 2023
8ff9151
review notification
phuang26 May 8, 2023
47c8efd
Resolve "molecular mass descriptor in sample metadata"
cllde8 May 8, 2023
bc85e51
Merge branch '536-molecular-mass-descriptor-in-sample-metadata' into …
phuang26 May 8, 2023
a7c51e9
Merge branch '537-review-notification' into 'server_chemotion_net-5'
phuang26 May 8, 2023
a1a1ca7
group default value
cllde8 May 9, 2023
afc49ab
rm review notification
phuang26 May 9, 2023
3c79b34
Merge branch '539-default-of-group' into 'server_chemotion_net-5'
phuang26 May 9, 2023
8cd7081
Merge branch '538-rm-review-notification' into 'server_chemotion_net-5'
phuang26 May 9, 2023
61a0c14
fix White Screen when clicking on Analysis DOI
cllde8 May 10, 2023
0783e94
Merge branch '540-white-screen-when-clicking-on-analysis-doi' into 's…
phuang26 May 10, 2023
7960181
fix white page while doi is null
cllde8 May 10, 2023
c0b706f
Merge branch '541-white-screen-when-clicking-on-analysis-doi' into 's…
phuang26 May 10, 2023
2f934d8
fix the incorrect license icon usage
cllde8 May 10, 2023
84a315f
Merge branch '542-incorrect-license-icon-usage' into 'server_chemotio…
phuang26 May 10, 2023
a362310
msg fix
phuang26 May 12, 2023
47a1aec
user reivew and svg fix
phuang26 May 16, 2023
ff0c912
Merge branch '544-user-review-fix' into 'server_chemotion_net-5'
phuang26 May 16, 2023
8a47436
remove log
phuang26 May 16, 2023
d94b307
group lead review update
phuang26 May 19, 2023
98a80b1
increase font size and add space
cllde8 May 23, 2023
b1a5848
Merge branch '547-sample-landing-page-style' into 'server_chemotion_n…
phuang26 May 23, 2023
8b49054
add comp-number to published sample page
cllde8 May 23, 2023
7b7d046
Merge branch '548-add-comp-number-in-sample-landing-page' into 'serve…
phuang26 May 23, 2023
9ac00fa
Merge branch 'server_chemotion_net-5' into '543-msg-fix'
phuang26 May 23, 2023
7ea552b
Merge branch '543-msg-fix' into 'server_chemotion_net-5'
phuang26 May 23, 2023
14b295c
Resolve "review ui reload issue"
phuang26 May 23, 2023
73a5711
Merge branch '546-review-ui-reload-issue' into 'server_chemotion_net-5'
phuang26 May 23, 2023
946e2e1
Resolve "compounds visibility"
cllde8 May 24, 2023
6331cbb
Merge branch '549-compounds-visibility' into 'server_chemotion_net-5'
phuang26 May 24, 2023
2f46e5f
anchor on publication page
cllde8 May 24, 2023
3e19a8b
Merge branch '550-anchor-on-publication-page' into 'server_chemotion_…
phuang26 May 24, 2023
ed60150
add solvent to sample metadata
cllde8 May 24, 2023
12212e2
Merge branch '552-add-solvent-to-sample-metadata' into 'server_chemot…
phuang26 May 24, 2023
8ee919e
published year
phuang26 May 24, 2023
ec4a5fe
Merge branch '553-published-year' into 'server_chemotion_net-5'
phuang26 May 24, 2023
b7ca735
linked-data
phuang26 May 24, 2023
4a7a178
Merge branch '551-linked-data' into 'server_chemotion_net-5'
phuang26 May 25, 2023
1ded334
add original id to compound list
cllde8 May 26, 2023
570e427
Merge branch '554-add-original-id-to-list' into 'server_chemotion_net-5'
phuang26 May 26, 2023
33a5af9
linked data api
phuang26 Jun 2, 2023
c8869e5
Merge branch '555-linked-data-api' into 'server_chemotion_net-5'
phuang26 Jun 4, 2023
e0bb2fa
fixed blank page issue on molecule archive after searching
cllde8 Jun 6, 2023
54d12ff
Repo update (#45)
phuang26 Jun 7, 2023
0bc42e2
remove unused file
phuang26 Jun 7, 2023
3ed6555
Update README.md
phuang26 Jun 7, 2023
51cd264
Update README.md
phuang26 Jun 7, 2023
a9732c2
Update README.md
phuang26 Jun 7, 2023
c7a4f1a
Update README.md
phuang26 Jun 7, 2023
ab5e21c
remove unused code
phuang26 Jun 12, 2023
18ca450
Update README.md
PiTrem Jun 12, 2023
18c4179
gate transfer
phuang26 Aug 5, 2022
9e3af15
Merge branch '489-gate-transfer-with-segments' into 'server_chemotion…
phuang26 Jun 13, 2023
0cb9e9b
revise readme file
cllde8 Jun 16, 2023
291a606
Merge branch '559-update-readme-file' into 'server_chemotion_net-5'
phuang26 Jun 16, 2023
c18e9ab
use ISO date format for publication data
cllde8 Jun 16, 2023
3c11ed6
change-cas-wording
phuang26 Jun 18, 2023
baf5fb4
Merge branch '560-iso-date-format' into 'server_chemotion_net-5'
phuang26 Jun 18, 2023
d1ce834
correct the date format at back end
cllde8 Jun 19, 2023
5f6aae6
lock element after submit
cllde8 Jun 25, 2023
2f2fb67
Merge branch '561-correct-the-date-format-at-back-end' into 'server_c…
phuang26 Jun 25, 2023
003fa2e
Merge branch '562-lock-element-after-submit' into 'server_chemotion_n…
phuang26 Jun 25, 2023
6f959e6
creation date of import
phuang26 Jun 26, 2023
d34a3a3
set license to CC BY as default
cllde8 Jun 26, 2023
3d07cb8
Resolve "physical properties"
cllde8 Jun 27, 2023
2123573
Merge branch '557-physical-properties-2' into 'server_chemotion_net-5'
phuang26 Jun 27, 2023
fcda88d
Merge branch '564-default-license' into 'server_chemotion_net-5'
phuang26 Jun 27, 2023
1b3e002
Merge branch '563-creation-date-of-import' into 'server_chemotion_net-5'
phuang26 Jun 27, 2023
abe4c93
Merge branch '556-blank-page-after-searching' into 'server_chemotion_…
phuang26 Jun 27, 2023
9076133
update yarn
cllde8 Jun 27, 2023
ddacb0b
Merge branch '566-update-yarn' into 'server_chemotion_net-5'
phuang26 Jun 27, 2023
d339b7a
.nvmrc
phuang26 Jun 27, 2023
8bb7c9d
introduce linked data component
cllde8 Jun 27, 2023
32e8dce
add info to lock element function
cllde8 Jun 27, 2023
433c7f2
Merge branch '565-linked-data-component' into 'server_chemotion_net-5'
phuang26 Jun 27, 2023
379b13e
Merge branch '567-add-info-to-lock-element-function' into 'server_che…
phuang26 Jun 27, 2023
c8d11b4
Merge conflict resolution
phuang26 Jun 28, 2023
e6f053e
remove unused code
phuang26 Jun 28, 2023
fd4bd9b
CHANGELOG
phuang26 Jun 29, 2023
7074b5f
Merge pull request #48 from ComPlat/repo_update_0623
phuang26 Jun 29, 2023
1e452bc
Bump json5 from 1.0.1 to 1.0.2
dependabot[bot] Jun 29, 2023
6fb1a11
Bump http-cache-semantics from 4.1.0 to 4.1.1
dependabot[bot] Jun 29, 2023
7d40399
Bump ua-parser-js from 0.7.26 to 0.7.35
dependabot[bot] Jun 29, 2023
5fc9d6d
Fix migrations to work with a fresh database
jochenklar Jul 13, 2023
76c0423
Fix seed to work with existing Person instances
jochenklar Jul 13, 2023
16e0554
Add a migration to create "public user"
jochenklar Jul 13, 2023
4174df9
Fix User.create_chemotion_public_collection
jochenklar Jul 13, 2023
4019616
Fix public api when no sample or reaction was published yet
jochenklar Jul 13, 2023
4e93d07
Fix Components when no sample or reaction was published yet
jochenklar Jul 13, 2023
3bb32c8
Add createNewSampleVersion functionality and linking of analysis cont…
jochenklar Jul 28, 2023
68d9b56
Add tags for previous and new version to samples
jochenklar Jul 28, 2023
120096a
Show NewVersion button only for publisher
jochenklar Aug 1, 2023
45396c6
Add links to Sample model
jochenklar Aug 6, 2023
ea07b27
Add links to analyses_tag when creating a new sample version
jochenklar Aug 6, 2023
02d9d8e
Update analyses tag when publishing a sample
jochenklar Aug 6, 2023
30dc087
Add submit_new_sample_version method
jochenklar Aug 9, 2023
4235db6
Add version_count to Doi model
jochenklar Aug 9, 2023
c331209
Only display new version button for latest version
jochenklar Aug 14, 2023
3c038f7
Add IsNewVersionOf to metadata_xml
jochenklar Aug 14, 2023
49e1ce7
Add analysis publication to submit_new_sample_version
jochenklar Aug 15, 2023
615b300
Fix issues with missing analyses on reactions
jochenklar Aug 28, 2023
a1b2d56
Fix missing includes in QuillEditor.js
jochenklar Aug 28, 2023
197b131
Fix seeds (create reaction root containers)
jochenklar Aug 29, 2023
8c0a640
Add NewVersion button and (incomplete) API for reactions
jochenklar Aug 29, 2023
a601863
Add link_analyses to create_new_reaction_version
jochenklar Sep 19, 2023
fc0e73b
Add create_new_sample_version to create_new_reaction_version
jochenklar Sep 22, 2023
56566c0
Add submit_new_reaction_version
jochenklar Sep 22, 2023
efe61f4
Update NewVersionButton style
jochenklar Oct 10, 2023
a94d3ed
Fix repository_api.rb
jochenklar Oct 10, 2023
48b626d
Use the same license for new version as for the previous versions
jochenklar Oct 10, 2023
296df21
Fix public user creation migration
jochenklar Oct 16, 2023
ee22dc0
Add versions_collection for new versions of published elements
jochenklar Oct 16, 2023
17fb8ba
Add version to short_label
jochenklar Oct 17, 2023
1c4e7b3
Fix collections for new versions
jochenklar Oct 31, 2023
460240f
Use "tag" icon for new version
jochenklar Oct 31, 2023
3266749
Refactor NewVersionModal and add it to ReactionDetails and SampleDetails
jochenklar Oct 31, 2023
c2679ac
Adjust styling
jochenklar Oct 31, 2023
4fd7e86
Fix NewVersionModal component
jochenklar Nov 3, 2023
ec640b2
Fix permission_level of versions_collection
jochenklar Nov 3, 2023
ae344d1
Do not duplicate samples when adding a new reaction version
jochenklar Nov 6, 2023
07bd446
Seal old samples for new reaction versions
jochenklar Nov 7, 2023
148ce46
Update submit new reaction version workflow
jochenklar Nov 7, 2023
60fa123
Create new version of a sample in a new reaction version
jochenklar Nov 7, 2023
8fcdd2a
Fix update_materials_for_reaction
jochenklar Nov 13, 2023
eec8eb7
Fix "Analysis ID" in RepoCommon.js
jochenklar Nov 17, 2023
c26b5b7
Fix element_submit helper method for links
jochenklar Nov 17, 2023
c2202d8
Submit new samples when submitting a new reaction version
jochenklar Nov 17, 2023
de000cd
Refactor NewVersionModal
jochenklar Nov 17, 2023
991c91d
Refactor redirect after new version is created
jochenklar Nov 17, 2023
95691bf
Create new version for scheme only reactions
jochenklar Dec 8, 2023
4633e4a
Submit new reaction versions
jochenklar Dec 8, 2023
aeff164
Fix assign_sample_to_collections
jochenklar Dec 8, 2023
56b2d5a
Add previous_scheme_only to reaction tag and update PublishReactionModal
jochenklar Dec 8, 2023
98d7684
Fix assign_sample_to_collections method
jochenklar Dec 12, 2023
7807ae7
Create new versions for analyses of new sample/reaction versions
jochenklar Dec 17, 2023
9561fad
Fix license for new sample versions
jochenklar Dec 18, 2023
d1ec346
Fix sample publication
jochenklar Dec 18, 2023
b3f821e
Fix NewVersionModal
jochenklar Dec 18, 2023
a1f3d4c
Create new links for new sample versions
jochenklar Dec 18, 2023
10ffc1c
Fix NewVersionModal
jochenklar Dec 18, 2023
0b6a397
Fix Material.js
jochenklar Dec 18, 2023
c415f6c
Delete new version from tags of previous version
jochenklar Dec 18, 2023
bb21fe2
Refactor NewVersionModal
jochenklar Jan 12, 2024
27c864a
Add create_new_reaction_samples_version to repository api
jochenklar Jan 12, 2024
48f4139
Refactor redirectAfterSubmit in NewVersionModal
jochenklar Jan 12, 2024
044b140
Remove redirectAfterSubmit in NewVersionModal and add specific actions
jochenklar Jan 16, 2024
2b753e3
Validate reaction in createNewSampleVersion in repository_api
jochenklar Jan 16, 2024
931fc16
Fix NewVersionModal
jochenklar Jan 22, 2024
827e41e
Add update_versions_tag to publishing concerns
jochenklar Jan 22, 2024
61ff760
Add VersionDropdown (for samples)
jochenklar Jan 26, 2024
1b10c14
Add VersionDropdown for reactions
jochenklar Jan 26, 2024
0ba3b40
Add id to version dropdown
jochenklar Jan 30, 2024
e9bc688
Adjust PublicAnchor for new DOI layout
jochenklar Jan 30, 2024
248b982
Fix submit_new_reaction_version
jochenklar Jan 30, 2024
c7c50ea
Fix literals duplication when creating new versions
jochenklar Apr 12, 2024
23fa5cf
Fix find_or_create_grouplead_collection when user is not a reviewer
jochenklar Apr 12, 2024
d06dca4
Use previous users and refs when submitting a new version
jochenklar Apr 12, 2024
a3c3f52
Fix display of old reaction versions
jochenklar Apr 19, 2024
dadb628
Remove publish_pending for new versions
jochenklar Apr 19, 2024
1e550aa
User previous users and refs when submitting new sample version
jochenklar Apr 19, 2024
73f952e
Allow for seperate versioning of reactions and samples again
jochenklar May 31, 2024
a32a50e
Allow to change ref on new reaction versions with old version samples
jochenklar Jun 7, 2024
5948189
Prevent creation of a new sample version when reaction is not changed
jochenklar Jun 7, 2024
1a43375
Add previously created new sample version to new reaction version
jochenklar Jun 7, 2024
d568b13
Fix display of old sample versions
jochenklar Jun 7, 2024
98b50c7
Cleanup create_new_reactions_samples_version code
jochenklar Jun 7, 2024
0076940
Fix create_new_sample_version
jochenklar Jun 7, 2024
156172b
Exclude already public samples from moving to the pending collection …
jochenklar Jun 7, 2024
49b32fe
Add replace_in_publication tag to indicate new sample versions without a
jochenklar Jun 7, 2024
92e8dfe
Fix disabling fields for new sample versions without new reaction ver…
jochenklar Jun 14, 2024
c44cfb6
Use reaction_id from tag for new sample versions without reaction
jochenklar Jun 14, 2024
6641bfd
Fix VersionDropdown
jochenklar Jun 14, 2024
563f637
Fix new sample version creation
jochenklar Jun 14, 2024
a089404
Fix version selection for sample versions on reaction publication page
jochenklar Jun 17, 2024
d24b63c
Add distinct to sample query
jochenklar Jun 18, 2024
9f764ca
Fix RenderAnalysisHeader
jochenklar Jun 18, 2024
16eea1f
Fix fix reactions list for old versions in publication view
jochenklar Jun 18, 2024
c23d882
Fix RenderAnalysisHeader
jochenklar Jun 18, 2024
3143dc7
Fix RepoReactionDetails
jochenklar Jul 11, 2024
38224c1
Fix handleDisplayReaction in PublicStore
jochenklar Jul 15, 2024
31a5d94
Fix handleGetReactions
jochenklar Jul 15, 2024
f88402d
Fix handleDisplayReaction
jochenklar Jul 19, 2024
f0942ec
Always show sample in review
jochenklar Jul 26, 2024
15e359d
Filter reaction sample versions to only show versions with a complete…
jochenklar Jul 26, 2024
52b991a
Do not run tag_as_published on new versions
jochenklar Jul 26, 2024
0add672
Fix resubmit button for new reaction versions
jochenklar Aug 5, 2024
7bedbb7
Remove new element version and doi when declined
jochenklar Aug 5, 2024
4f13ad3
Check previous version in process_element
jochenklar Aug 9, 2024
ae71279
Fix ReviewPublishBtn
jochenklar Aug 9, 2024
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10 changes: 0 additions & 10 deletions .babelrc.bak

This file was deleted.

35 changes: 0 additions & 35 deletions .env.development

This file was deleted.

8 changes: 0 additions & 8 deletions .env.production.example
Original file line number Diff line number Diff line change
Expand Up @@ -29,11 +29,3 @@ DEVISE_NEW_ACCOUNT_INACTIVE=false
# Application's title
APPLICATION_TITLE='Chemotion'

DATA_CITE_BASE_URI=https://api.test.datacite.org
DATA_CITE_PREFIX=prefix
DATA_CITE_API_USERNAME=username
DATA_CITE_API_PASSWORD=password
DATA_CITE_DEVICE_PREFIX=DEVICE-
DATA_CITE_RESEARCH_PLAN_PREFIX=RP-
DATA_CITE_DEVICE_PUBLISHER=chemotion.net
DATA_CITE_DEVICE_CREATOR=chemotion.net
11 changes: 0 additions & 11 deletions .env.test
Original file line number Diff line number Diff line change
Expand Up @@ -18,14 +18,3 @@ DEVISE_DISABLED_SIGN_UP=''

# Any new account to be inactive by default => only admin can (de)activate
DEVISE_NEW_ACCOUNT_INACTIVE=false

DATA_CITE_BASE_URI=https://api.test.datacite.org
DATA_CITE_PREFIX=prefix
DATA_CITE_API_USERNAME=username
DATA_CITE_API_PASSWORD=password
DATA_CITE_DEVICE_PREFIX=DEVICE-
DATA_CITE_DEVICE_PUBLISHER=chemotion.net
DATA_CITE_DEVICE_CREATOR=chemotion.net

# uncomment for headfull testing
# USE_HEAD=:D
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