Code

Development#303

Code

Merged

CS76 merged 173 commits intomainSteinbeck-Lab/coconut:mainfrom developmentSteinbeck-Lab/coconut:developmentCopy head branch name to clipboardDec 4, 2024

+14,988-2,357

Commits

Commits on Aug 20, 2024

• feat: assign DOIs to collections

  NRayya

  committed
  0d6acf3

Commits on Aug 26, 2024

• Merge branch 'development' into doi

  CS76

  committed
  2571cf1

Commits on Sep 12, 2024

• fix: added repository

  CS76

  committed
  d0652b3

• fix: added missing command

  CS76

  committed
  a0c8dd8

• fix: added yes flag to install commands

  CS76

  committed
  2f53219

• fix: AttributeError: 'NoneType' object has no attribute 'people' fix

  CS76

  committed
  56433df

• fix: added required libs

  CS76

  committed
  f46711e

• fix: removed python2 to resolve Package 'python2' has no installation candidate

  CS76

  committed
  668d489

• fix: enabled php redis

  CS76

  committed
  996baa4

• fix: removed rename

  CS76

  committed
  275330b

• fix: added missing media drop

  CS76

  committed
  e10f109

• Merge branch 'feature-doi-service' into doi

  Show description for b3afd7a
  CS76

  committed
  b3afd7a

• fix: DOI issue fixed

  CS76

  committed
  b03eae8

Commits on Sep 18, 2024

• wip: suggested changes are now stored in the reports table. SQL queries need to be built at the time of approving the report

  sriramkanakam87

  committed
  2a5c5f5

Commits on Sep 23, 2024

• Merge pull request #257 from Steinbeck-Lab/main

  Show description for c4df3c0
  CS76

  authored
  c4df3c0

• Merge branch 'development' into doi

  CS76

  committed
  063f0fe

• fix: key issue fixed

  sriramkanakam87

  committed
  2da1fcf

Commits on Sep 24, 2024

• fix: disabled logging empty values and enabled handling of existing empty values in both old and new columns

  sriramkanakam87

  committed
  bef6b8d

• fix: now the timestamps are auto managed for the pivot table molecule_sample_location

  sriramkanakam87

  committed
  b6067a5

• wip: suggested changes are now stored in the reports table. SQL queries need to be built at the time of approving the report

  sriramkanakam87

  committed
  5be9ccb

• Merge branch 'feat-report-suggestions' of https://github.com/Steinbeck-Lab/coconut into feat-report-suggestions

  sriramkanakam87

  committed
  dc88750

Commits on Sep 26, 2024

• feat: improved suggestions by replacing the old key value pairs with tabs that can be approved by curators

  sriramkanakam87

  committed
  058d942

• fix: now the time line shows synonym and cas changes properly

  sriramkanakam87

  committed
  716fe43

• chore: commented out the slide over (wip)

  sriramkanakam87

  committed
  d7dbc88

• fix: minor fix related to creating citations

  sriramkanakam87

  committed
  ff4621b

Commits on Sep 29, 2024

• feat: improved the user friendliness (wip)

  sriramkanakam87

  committed
  8fef446

Commits on Sep 30, 2024

• feat: added np_classifier in compound details and history ui updates

  CS76

  committed
  3c97f6b

• fix: disabled history show by default and header to represent the event

  CS76

  committed
  afa3037

• chore: pint updates

  CS76

  committed
  24f56cb

• feat: force https redirect and docker compose prod updates

  CS76

  committed
  6735e6d

• fix: horizon gate updates

  CS76

  committed
  bec1e4c

• fix: sail network issue fix

  CS76

  committed
  74ab411

• fix: updated root folder

  CS76

  committed
  1cd3680

• fix: nginx default config updates

  CS76

  committed
  667912a

• fix: reverted docker compose build approach

  CS76

  committed
  9708ddd

• fix: sail network issue

  CS76

  committed
  36b0139

• Merge branch 'development' into dc-prod

  CS76

  committed
  3ca326c

• fix: app name conflict issue fix

  CS76

  committed
  411916b

• fix: audit fix

  CS76

  committed
  2b3f5f5

Commits on Oct 1, 2024

• feat: the report changes form is made user friendly with pre-filled fields

  Show description for 96b2dc8
  sriramkanakam87

  committed
  96b2dc8

• feat: enabled create time pop-up modal to display overall changes being requested

  Show description for 2c1149f
  sriramkanakam87

  committed
  2c1149f

• feat: altered the edit and view pages to load the new structure of the suggested changes

  Show description for 8f8113d
  sriramkanakam87

  committed
  8f8113d

• feat: new helper functions and fixes to the old ones to accommodate report suggestions workflow.

  sriramkanakam87

  committed
  bc36e7d

• feat: now timeline can handle citations

  sriramkanakam87

  committed
  cceba8e

• chore: removed dd statements.

  sriramkanakam87

  committed
  ae4bd28

Commits on Oct 2, 2024

• fix: typo

  Kohulan

  committed
  dbf6c0d

• fix: conditional checks were refined to work with the data structures of audits.

  sriramkanakam87

  committed
  87363b3

• fix: to capture audits from citations

  sriramkanakam87

  committed
  54bc73f

• fix: additional checks

  sriramkanakam87

  committed
  c71fbc2

• fix: key issue fixed

  sriramkanakam87

  committed
  ceba3a9

• fix: disabled logging empty values and enabled handling of existing empty values in both old and new columns

  sriramkanakam87

  committed
  f858ec0

• fix: now the timestamps are auto managed for the pivot table molecule_sample_location

  sriramkanakam87

  committed
  6396ce9

• wip: suggested changes are now stored in the reports table. SQL queries need to be built at the time of approving the report

  sriramkanakam87

  committed
  cb40e70

• wip: suggested changes are now stored in the reports table. SQL queries need to be built at the time of approving the report

  sriramkanakam87

  committed
  367e9ca

• feat: improved suggestions by replacing the old key value pairs with tabs that can be approved by curators

  sriramkanakam87

  committed
  49b918d

• fix: now the time line shows synonym and cas changes properly

  sriramkanakam87

  committed
  5a669cc

• chore: commented out the slide over (wip)

  sriramkanakam87

  committed
  51510be

• fix: minor fix related to creating citations

  sriramkanakam87

  committed
  b75caa4

• feat: improved the user friendliness (wip)

  sriramkanakam87

  committed
  1475c47

• feat: the report changes form is made user friendly with pre-filled fields

  Show description for f650aee
  sriramkanakam87

  committed
  f650aee

• feat: enabled create time pop-up modal to display overall changes being requested

  Show description for 97a11db
  sriramkanakam87

  committed
  97a11db

• feat: altered the edit and view pages to load the new structure of the suggested changes

  Show description for 0f2acbe
  sriramkanakam87

  committed
  0f2acbe

• feat: new helper functions and fixes to the old ones to accommodate report suggestions workflow.

  sriramkanakam87

  committed
  ed645af

• feat: now timeline can handle citations

  sriramkanakam87

  committed
  6c1c1aa

• chore: removed dd statements.

  sriramkanakam87

  committed
  0eb2497

• Merge branch 'feat-report-suggestions' of https://github.com/Steinbeck-Lab/coconut into feat-report-suggestions

  Show description for b28d1fa
  sriramkanakam87

  committed
  b28d1fa

• feat: now only the fields requested for changes are available and the rest are disabled in edit page

  sriramkanakam87

  committed
  206dc4b

• feat: updated october 2024 release

  CS76

  committed
  3e7733b

• fix: the disabling of non-suggested fields is restricted only to edit

  sriramkanakam87

  committed
  7e83f7b

• fix: saving the overall suggested changes so that they are available in both the original and curator jsons

  sriramkanakam87

  committed
  607535c

• feat: original suggestions are saved and never touched, instead a separate copy is made available for curators to work on

  sriramkanakam87

  committed
  9c2d3f3

• fix: deleted the old statement

  sriramkanakam87

  committed
  31ddfb0

Commits on Oct 7, 2024

• fix: auto flush removed for dash widgets and geo-locations' widgets get the data on the fly when the page is accessed.

  sriramkanakam87

  committed
  9ad6641

• chore: formatting changes

  sriramkanakam87

  committed
  3ce816a

• fix: the status of the molecule now sets to revoked while deactivation

  sriramkanakam87

  committed
  a275b02

• feat: observer is created on molecule model to flush the model from cache after update

  sriramkanakam87

  committed
  f56ef21

• chore: refactored the code

  sriramkanakam87

  committed
  0dc5535

Commits on Oct 8, 2024

• fix: which items received approval is now saved when approved, no need to save the form before approval

  sriramkanakam87

  committed
  53847b0

• fix: redirect to view page after the report is approved

  sriramkanakam87

  committed
  0ded278

• fix: save modal is only displayed if it is a change

  sriramkanakam87

  committed
  5670f31

• fix: saving doi for reporting

  sriramkanakam87

  committed
  658ff2f

Commits on Oct 9, 2024

• Merge pull request #265 from Steinbeck-Lab/fix-molecule-deactivation-status

  Show description for 352f25f
  CS76

  authored
  352f25f

• Merge pull request #266 from Steinbeck-Lab/feat-flush-molecule-cahce-on-update

  Show description for 3af830d
  CS76

  authored
  3af830d

• Merge pull request #262 from Steinbeck-Lab/fix-dashwidgets-autoflush-removal

  Show description for 9345d1d
  CS76

  authored
  9345d1d

• Merge pull request #260 from Steinbeck-Lab/dev-kohulan

  Show description for 3ebdecc
  CS76

  authored
  3ebdecc

• fix: removed cache flush from the coconut cache command

  CS76

  committed
  fa75c27

Commits on Oct 10, 2024

• fix: various fixes to the reporting workflow

  sriramkanakam87

  committed
  ca3dfdf

• feat: now IUPAC names are displayed with proper italicisation.

  sriramkanakam87

  committed
  c2d3c52

Commits on Oct 13, 2024

• fix: to handle italicised display of iupac name when name is not available

  sriramkanakam87

  committed
  22187a3

Commits on Oct 14, 2024

• Merge pull request #271 from Steinbeck-Lab/feat-italic-display-of-iupac-names

  Show description for b37dde6
  Kohulan

  authored
  b37dde6

• fix: copy buttons now have a time out of 4 seconds to reset

  sriramkanakam87

  committed
  335fdc2

• feat: a download option is provided for the respective mol files from CDK and RDKit

  sriramkanakam87

  committed
  662cd84

• feat: on hover now indicates which source the file is being downloaded from

  sriramkanakam87

  committed
  46c3a16

• feat: now the search allows for partial inchikey search

  sriramkanakam87

  committed
  10711c4

• Merge pull request #273 from Steinbeck-Lab/feat-download-molfile

  Show description for be91376
  Kohulan

  authored
  be91376

• Merge pull request #272 from Steinbeck-Lab/fix-copy-button-timeout

  Show description for cc62abf
  Kohulan

  authored
  cc62abf

• Merge pull request #274 from Steinbeck-Lab/feat-partial-inchikey-search

  Show description for 2e04d2b
  Kohulan

  authored
  2e04d2b

Commits on Oct 15, 2024

• fix: references to the compounds' source links are correctly parsed and displayed.

  sriramkanakam87

  committed
  43b88f7

Commits on Oct 16, 2024

• Merge pull request #278 from Steinbeck-Lab/fix-collection-reference-links

  Show description for ba506f0
  Kohulan

  authored
  ba506f0

• fix: to open reporting in a new tab

  sriramkanakam87

  committed
  3f999a4

• Merge pull request #279 from Steinbeck-Lab/fix-open-reporting-in-new-tab

  Show description for 9d068f0
  Kohulan

  authored
  9d068f0

• fix: the request now goes to rdkit instead of opedbabel which was throwing bad gateway error.

  sriramkanakam87

  committed
  7e0fe0f

• Merge pull request #281 from Steinbeck-Lab/fix-3d-depict

  Show description for 35d10a1
  Kohulan

  authored
  35d10a1

Commits on Nov 5, 2024

• fix: cookie consent privacy and terms of use links are pointed to the proper routes

  sriramkanakam87

  committed
  c2c4b49

• Merge pull request #287 from Steinbeck-Lab/fix-cookieconsent-links

  Show description for 636d8d9
  Kohulan

  authored
  636d8d9

Commits on Nov 6, 2024

• fix: refactored the form into the Citations model and applied a minor fix to creating citations.

  sriramkanakam87

  committed
  efab97f

• feat: molecule citation relation can now be searched by doi as well to attach citations to the molecule.

  sriramkanakam87

  committed
  71645e5

• feat: now citations can be searched by doi from the report's molecule relation manager.

  sriramkanakam87

  committed
  0726de4

Commits on Nov 7, 2024

• feat: new column assinged_to is added to the reports table

  sriramkanakam87

  committed
  0e3278b

• feat: relation to retrieve the assigned user is added to the user model

  sriramkanakam87

  committed
  2cabe52

• feat: users with any roles can now assign reports for curation

  sriramkanakam87

  committed
  6987ddf

• fix: only assigned users now have access to edit view of reports

  sriramkanakam87

  committed
  0c2af60

• fix: users can not edit the submitted reports and creation time null report record is handled.

  sriramkanakam87

  committed
  ed4e0d1

Commits on Nov 12, 2024

• feat: added foreign key on structures table linking it to molecules table and added the relation in the models

  sriramkanakam87

  committed
  fe580af

• feat: new command to import the 2d SDFs into structures table

  sriramkanakam87

  committed
  1569b81

• feat: audits on the structures table are added to the timeline

  sriramkanakam87

  committed
  a4109d8

Commits on Nov 13, 2024

• fix: 2d download is now fetched from the db

  sriramkanakam87

  committed
  8ac4729

• feat: download button for 3d molecules is now available

  sriramkanakam87

  committed
  42c0274

• fix: links in the footer are now working

  sriramkanakam87

  committed
  82fa0b9

• fix: conditional hidden issue fix

  CS76

  committed
  bf48f25

• fix: access restrictions and improved user-friendliness

  sriramkanakam87

  committed
  3826800

Commits on Nov 14, 2024

• wip: 3d depiction

  sriramkanakam87

  committed
  efca0a4

Commits on Nov 15, 2024

• feat: new command to fix duplicates and missing links for the molecules pointing to the source datasets online.

  sriramkanakam87

  committed
  efd4626

• fix: hidden field issues are fixed

  sriramkanakam87

  committed
  8d224dd

Commits on Nov 18, 2024

• feat: new command to import a set of jsons in a folder

  sriramkanakam87

  committed
  be708bc

Commits on Nov 19, 2024

• fix: fixed the file name issue

  sriramkanakam87

  committed
  5893c54

• fix: reverted to pinging the api for now

  sriramkanakam87

  committed
  a061a35

• fix: removed the toolkit as we are only using RDKit

  sriramkanakam87

  committed
  c373d45

Commits on Nov 20, 2024

• fix: the missing molecules are excluded

  sriramkanakam87

  committed
  905f092

• fix: replaced the or with and condition

  sriramkanakam87

  committed
  885c2db

• feat: users with any role can now see an additional filter tab assigned. The rest of the queries are scoped as per the access privileges.

  sriramkanakam87

  committed
  21838e9

• fix: curators can only see open reports in the assigned tab

  sriramkanakam87

  committed
  ddde34b

Commits on Nov 21, 2024

• fix: fixes the array for the parents

  sriramkanakam87

  committed
  1ba14ec

Commits on Nov 22, 2024

• Merge pull request #289 from Steinbeck-Lab/feat-report-curator-assignment

  Show description for 728fc92
  CS76

  authored
  728fc92

• Merge pull request #288 from Steinbeck-Lab/fix-attach-citation-searchby-doi

  Show description for 91461df
  CS76

  authored
  91461df

• chore: rearranged the look and descriptions of the download

  sriramkanakam87

  committed
  e9947a3

• Merge branch 'development' into feat-report-suggestions

  Show description for f1ada25
  CS76

  committed
  f1ada25

• Merge pull request #267 from Steinbeck-Lab/feat-report-suggestions

  Show description for 4bed61d
  CS76

  authored
  4bed61d

• fix: enabled cookie banner display on smaller screens

  CS76

  committed
  b6c4d6b

• feat: enabled mol / sdf drag drop

  CS76

  committed
  fe0b4f6

• Merge pull request #293 from Steinbeck-Lab/fix-cookie-banner

  Show description for 905e118
  sriramkanakam87

  authored
  905e118

• feat: added list view

  CS76

  committed
  1341264

• Merge pull request #294 from Steinbeck-Lab/feat-drag-drop-mol

  Show description for 9aa24ba
  sriramkanakam87

  authored
  9aa24ba

Commits on Nov 23, 2024

• fix: various fixes to handle null values and to hide the report/suggestion options altogether.

  sriramkanakam87

  committed
  186d23c

• Merge pull request #295 from Steinbeck-Lab/feature-results-table-view

  Show description for 78c57f6
  CS76

  authored
  78c57f6

• Merge pull request #290 from Steinbeck-Lab/fix-links-terms-usage

  Show description for fa86da0
  CS76

  authored
  fa86da0

Commits on Nov 25, 2024

• feat: python script for uploading collection wise sdfs

  sriramkanakam87

  committed
  aa6db10

• chore: code optimisation

  sriramkanakam87

  committed
  a77cb3d

• fix: added another argument for giving base directory

  sriramkanakam87

  committed
  2d66702

• fix: default base dir is the current working directory

  sriramkanakam87

  committed
  1ab3f9a

• feat: added SDF download link to collection details page and ui bug fixes on data-sources views

  CS76

  committed
  4b2d56b

• Merge pull request #296 from Steinbeck-Lab/feat-upload-collection-sdfs

  Show description for d97501d
  CS76

  authored
  d97501d

Commits on Nov 26, 2024

• fix: handles null values during approvals, fixes curator access issues and report approval errors

  sriramkanakam87

  committed
  4f661a8

Commits on Nov 27, 2024

• fix: bulk activate and de-activate is fixed

  sriramkanakam87

  committed
  13a0997

• fix: optimised the code with indexes and batches

  sriramkanakam87

  committed
  48b6f8a

Commits on Nov 28, 2024

• feat: enabled basic implementation of search

  CS76

  committed
  4dbede1

• Merge pull request #298 from Steinbeck-Lab/fix-collection-compound-links

  Show description for 033903a
  CS76

  authored
  033903a

• Merge pull request #297 from Steinbeck-Lab/feat-report-suggestions

  Show description for a38339b
  CS76

  authored
  a38339b

• Merge pull request #291 from Steinbeck-Lab/feat-import-2D-3D-SDFs

  Show description for caf0c55
  CS76

  authored
  caf0c55

• Merge pull request #300 from Steinbeck-Lab/feat-advanced-search

  Show description for 00340b9
  sriramkanakam87

  authored
  00340b9

• fix: updated citation

  CS76

  committed
  67af50d

Commits on Dec 2, 2024

• fix: updated readme

  CS76

  committed
  73380ae

• Merge branch 'development' into doi

  CS76

  committed
  a8eef52

• fix: updated coconut collection assign doi command updated

  CS76

  committed
  6fd1a71

• chore: code formatting updates

  CS76

  committed
  d3fb756

• fix: DOI issues fix

  CS76

  committed
  916cc60

• fix: enabled DOI links on collection pages

  CS76

  committed
  a3b1b5f

• feat: added all the available columns from molecules and properties tables to facilitate api search

  sriramkanakam87

  committed
  f93caa5

• fix: corrected the fillable arrays inline with production db

  sriramkanakam87

  committed
  beadcb8

Commits on Dec 3, 2024

• Merge branch 'development' into feat-api-search-expansion

  sriramkanakam87

  committed
  8cb0379

• Merge pull request #301 from Steinbeck-Lab/feat-api-search-expansion

  Show description for 5e659bb
  CS76

  authored
  5e659bb

Commits on Dec 4, 2024

• chore: updated readme

  sriramkanakam87

  committed
  5d1e1a2

• Merge pull request #302 from Steinbeck-Lab/chore-docs-update

  Show description for 0f4145c
  CS76

  authored
  0f4145c