Releases v1.0.0
1.0.0 (2024-09-12)
Features
a command to refresh widgets of dashboard, collections and geolocations (not those of molecules and organism) (2e97965 )
a new command for updating the number of molecules each organism has. (16994e7 )
a new script is now available to update the auto increment columns (13378b3 )
add assign identifiers command (174e96e )
added bioschema to molecule pages (3ccfdb2 )
added button for publishing the collection. (98d3ba4 )
added chembl name importer (8fa1c88 )
added command to generate api docs (75e2121 )
added copy to clipboard button (884fe74 )
added default sort and tags for report resource (9c3e22b )
added docs and other command updates (2380fbf )
added functionality to display the status of the collection (e14219b )
added new columns to sample location tables (00f7e68 )
added NPAtlas import script, annotations score species scoring updates, docker file updates to install bcmath (28c4ceb )
added organism and citation search (368fd97 )
added relationship managers for report resource as well as one for audits. (d2278a6 )
added search to landing page (757c5e1 )
added SEO (34a62d9 )
added structure editor (ca53f30 )
added view report functionality to allow user to view the report after receiving mail confirmation. (82f4a9a )
added vitepress docs (b7fddc8 )
advanced filters are now available on molecules (69252cd )
advanced filters are now available on organism table (6d69142 )
all the models are now auditable (7d84f6f )
allow activation and deactivation of molecules (f704256 )
assign identifiers to collections (ee60475 )
bug fixes and other updates (6772b7c )
bulk activate and deactivate of molecules is now available (497727e )
ChEBI names importer is now available (6ecf269 )
collections in the search page can also now show display images (c7658ed )
compound time line is now available (b844ba8 )
Create bug_report.yml (5de141f )
Create natural_products_submission.yml (8f1b74f )
created a separate widget for molecules in the dashboard (18e57cb )
created a view for collection and added widgets (c4d7282 )
created dashboard widgets for all resources (709e21c )
created geolocation and organism resources (294a25c )
created geolocation and organism resources and their relation managers for molecule resource (c51050c )
created molecule relation manger for collection resource, added functionality for processing molecules in entries table, and added forget the collection molecules count at the end of import (6130df4 )
created relationship managers for geolocation and organism (0cb7652 )
created view page for geolocation and added widgets (be02cd8 )
created view page for molecule and added widgets (a5bc781 )
created view page for organism and added widgets (7562377 )
db schema is updated and now linked to info.coconut account (ae86e9f )
display images can be uploaded to collections (2894396 )
displays the counts of resources by the side (641ea96 )
displays tool tips for the report fields (041b1bd )
displays various counts in the collection table and added two widgets in collection stats (698184c )
doi fetching in citation (wip) (8f43650 )
enable local docker composer prod deployement (edb928b )
enabled cache and various bug fixes (97f9acb )
enabled REGAPP SSO (fb97420 )
enabled SEO meta tags, organisms search page and other small updates (caf2acb )
enabled structure editor - paste from clipboard (58aeeab )
extend Bioschemas metadata (11ce7ca )
generated policies for geolocation and organism (35d1d1d )
history of the compound is now available in the compound details page (bc26426 )
home page collection cards will now display images (1e6aac1 )
implemented advanced tables and various other minor updates (3afe3f7 )
implemented citations, collections, organisms rest controllers and corresponding resources (4b9e8ae )
implemented REST API service and swagger documentation, migrated from l5-swagger to lomkit (bf20706 )
implemented social login, ui updates and bug fixes (428a201 )
improved the user friendliness of the command using prompts (d405d60 )
iri and rank fields are now available in the forms for organism (8ef926a )
IRI is now displayed below rank and is clickable (a1ff54d )
landing page updates (036eb3d )
molecule relation manager for sample locations is now available (9b0c1fe )
molecule_reporting_template.yml (668284e )
molecules of an organism can now be moved to another organism including to a specific part of this organism (df5cd10 )
moved the updated docs into the coconut repository (af21601 )
new columns are made available and filters are tuned (6260958 )
new command to copy names from entries and add them to synonyms for all the molecules (4f1988a )
new docs (2b2e433 )
new interactive command to reassign molecules to a selected organism from the list of duplicates based on slug (7adb664 )
new pages added (4ecf171 )
new registrations can now provide additional data like orcid, username, affiliation, etc (31555c0 )
new slug column is added to organisms table (2d268c3 )
now users can add collections, molecules or citations while creating the report itself (022a4c3 )
now users can skip a group of records and proceed to the next (af543ec )
now users can suggest changes to the properties of molecules, citations, collections and organisms (313b736 )
now users have to provide a reason for deactivating molecules (07248d4 )
now users receive new mail after reporting (5f93e7c )
part of previous commit (5fdc58d )
pdf download is now available for user views (c2642e9 )
prod build (925c2ec )
reporting of molecules can now be done from molecules table and restructure of the table for better user experience (9614fb0 )
resolved issues with open-api documentation, resources updates and basic api testing done (9cfcb4e )
sample location relation manager for organism is now available (8d2b947 )
sample location resource is now available but not in navigation (104ad85 )
sample_locations table is now available in place of organism_parts and a few more columns are also made available to store collections data (c8e80fe )
scheduled a refresh of cache for dashboard widgets (d825bc3 )
search updates and other minor changes (4203ab2 )
shows active and inactive molecules in separate views with advanced filters enabled (a98ac14 )
shows the related organisms in the relations in edit mode (8ebfb66 )
similar named organisms are displayed on the edit page of organisms with an option to edit them (36622d4 )
the new fileds in registrations are also now available in profile updation (2e1fe7f )
unified search options across pages, default search caching, mobile screen bug fixes (de6e6f5 )
updated logo (96715fc )
updated pagination logic and added loading screen while fetching results. fixes #220 (7fabdd4 )
user views can now be exported in various spread sheet formats (710f0c4 )
ux/ui updates, text changes and commands added (3b84e5d )
various updates and bug fixes (9b3cac4 )
various ux/ui updates and other minor changes (822760b )
Bug Fixes
3d rendering login updates, various other small updates (ed75cf0 )
a new column for counting molecules is now added to organisms table (50b1221 )
abbreviation correction (92e7e85 )
abbreviation correction for coconut (efe3d38 )
abbreviation of coconut is fixed (1e58f8e )
accessibility issues resolved and also enabled source maps (b9fad04 )
add chembiosys about.blade.php (cc04cf9 )
add more button when synonyms are available and above certain count (3e1197c )
add zenodo logo README.md (a2b7c3c )
added a csv column to reports table to avoid preloading in the form (191c605 )
added a new migration for new columns of user and filling name with first and last names (1fcf7eb )
added cache policy for images and also updated links in application logo (87295ca )
added cache to welcome page (ceaa44b )
added checks for the creation of report (28d01b3 )
added composer private repo install capabilities (00d4c22 )
added css from vendor folders (a894fad )
added gzip compression (faf9c9c )
added img alt text (96cd466 )
added IRI link to the organisms table (ff6df46 )
added local env variable to allow proper redirection (cee868e )
added matomo scripts to layout pages (2f051ad )
added missing bcmath extension to php docker container (5a83108 )
added missing libraries (20d6b23 )
added preview link to structure image (055e66b )
added remove duplicates command (4bda2f8 )
added support for old coconut urls (f7d8eed )
added transparent favicon (163e683 )
added variety of checks to hide and/or edit fields in accordance with the operation on report resource form (2ac35ca )
added view more button to compound details page and other minor improvements (18eddbe )
adding full path (dd8a692 )
adjusted collection width on home page (d96e5a7 )
all the values caches are set to expire after 2 days. (847137f )
anchor with in anchor bug fix (45720f6 )
annotation score calc updates (9eb6684 )
applied filament excel patch (ece837e )
broken classification links fix (5ba0554 )
bug fixes in schema and other updates to 3d rendering (ce4b9f9 )
build deployment (6d15b0d )
cache and search filters update and bug fixes (fe82ab1 )
cache applied to collection resource widgets (18aba41 )
cannot access offset of type string on string bug fix (840404b )
changed molecule entry filed to text area and formatting changes (c7c842e )
citation introduction.md (df9d916 )
class name "ImportSTOUTIUPACNames" update - build failure (eff9ac3 )
classes are now made clickable which open corresponding searches in new tab (2d89b6b )
cleaned up spatie media remnants (a268a53 )
code refactoring and performance improvements (8743bab )
collection image updates (ee160e9 )
collections image override bug fix and auditables relation manager bug fix (a35bb25 )
column altered to handle empty name (3b831eb )
composer_auth var added (4387da4 )
compound details page updates, search updates and other minor changes (e53ddb7 )
compound details page, header link updates and annotation score code formatting (ad443a0 )
concatenating 0 to the cnp id (b32f65b )
conditional toolkit rendering enabled on molecular 2d views (0d225bb )
correct name for the command (d67dd04 )
css updates fix (a35eac3 )
dash widgets molecules count (3fa7a8d )
dashboard logo link is now pointed to homepage. fixes #157 (306510b )
database count introduction.md (589ff33 )
database schema display (1795c15 )
deactivation is only visible for super-admins (e18fc03 )
default user avatar is now generated using first and last names (c9fd00c )
delete .DS_Store (158d94c )
delete organisms with no molecules and enables audit trail (7ca9c65 )
details in about page are updated to be accurate. (dab0557 )
DFG logo README.md (30e37c7 )
disabled rest authorisation cache (61ad3bc )
display organisms list (e6763bc )
displaying revoked molecule details on the web page (df336a9 )
download page css updates (104f17b )
drop shadow introduction.md (e010def )
enabled auditing (7a88fbe )
enabled edits of citations. (7837d5d )
enabled https redirect and also gzip compression (5c74027 )
enabled lazy loading in the welcome page (57be610 )
enabled tautomeric standardization, various import scripts and other updates (14b005a )
enforcing url https redirect (b0fdbc9 )
filament route missing issue fix and composer update changes (edf2dbd )
file path missing bug fix (00aec98 )
formatting updates (c6d9318 )
formatting updates (8d836dc )
formatting updates and other changes (672f8fc )
gave view access to normal users for geolocations and organisms resources (aa4c86c )
header issue and other minor css changes (61606ad )
header issues resolved, tag line updates and other small bug fixes (644a319 )
if the doi fetch fails to get data from the apis, it will also search coconut db (4b7eeeb )
import preset path fix (0cd86e9 )
importer updates and formatting changes (d8bd65e )
imporved introduction and statistics (d07515e )
improve documentation visualization (6e7f3de )
improved readability of the event and affected columns (acb688c )
improved README.md (7e18df0 )
improvements to the time line display in the compound details page (01ad02d )
include analysis (be5f0c6 )
include licensing information (e241809 )
introduced toggle buttons (583e295 )
layout updates on 2d rendering (ef0ecdc )
list table and widgets of collection resource were pointed to the columns instead of cache (c71ccc8 )
loading fonts locally (54b73fb )
logo path index.md (04bd35c )
logo shadow introduction.md (29c8d83 )
made audits as the default tab for the report view after clicking on the button in the mail for status changes and removed unnecessary details in the mail templates. (df4a61d )
malformed auth.json bug fix (a669d6e )
merge conflicts from development (208e980 )
minor molecule card updates (2ce5b9d )
minor updates (2ce527d )
minor updates and access panel logic added (346f292 )
missing collection name in social card bug fix (9f63111 )
missing file in the path bug fix (d4c856c )
missing files bug fix (d394a55 )
missing identifiers now returns 404 and also added hasvariants logic to molecule details page (48c5a4d )
missing imports and can access panel (a64b2a0 )
missing index.css file bug fix (b48fa4a )
molecule details page update, iupac names import command added, header changes (26fa0b7 )
more lazy loading optimisations (9ebdd45 )
more optimisation (6a19b77 )
more updates (852e227 )
more updates to header (535aa85 )
nginx docker fail bug fix (cddf6ce )
nginx path update (0ab8a80 )
now only the similar organism names with any molecules attached to them are displayed in the organism edit page's side panel (60a840d )
now report relations are shown according to the report type (492d700 )
now users have to provide affiliation details (3645fc5 )
npm security fix and other build files (91709a5 )
npm update (1e2c4f0 )
null synonymns bug fix (6e894b9 )
OCL loading issue fix (ac18255 )
organism name has to be unique in the table (4687194 )
organisms in search listing updated (6f0cf24 )
pagination dark mode css removed (40800c6 )
parameterised the molecule in the frontend livewire view (48edf84 )
path issues fix (2f4d64e )
performance improvement for dashboard widgets using raw queries. (9ae31bf )
performance improvement for widgets in collections, geolocations, molecules, organisms (6c00b12 )
published assets, prod build and composer lock update (38530fd )
queries in collection and geolocation stats inline with app cache refresh (9506316 )
query switched to unique cannonical smiles, other bug fixes and updates (319c64a )
ReadME (4c83bad )
reason from reports table is removed since there is a column comment that curators can use (37c1c50 )
recent molecules filtering updates (465672a )
recent molecules max width and mobile nav bar missing links added (50dda62 )
Redis not found bug fix (392080f )
remove SSL config since its configured using GKE ingress (bbcaa49 )
removed avatar field for collections (259846e )
removed flush db command (ad22b40 )
removed FLUSHDB (e448340 )
removed python2 (56b0a45 )
replaced the column molecular_weight with exact_molecular_weight and added a helper tool tip to mention the source of calculation (b880c46 )
reset nginx conf (f47eac6 )
reset previous commits (ffea98a )
resolved #117 issue and default query update (c6d24fc )
resolved #6 (3040e20 )
resolved all text area import instances (90eb367 )
resolved dark mode (19c52c2 )
resolved molecule route issue (2c451b0 )
resolved npm issues (5fc491c )
resolved structure editor overlap, other minor updates (ba43250 )
resolves #169 (630a9a0 )
resolves issue #136 (3f628d7 )
search is now limited to specific columns and new formatting changes for php class instantiation (bf93081 )
search organism by name query update (6e0d614 )
search updates (f4d76be )
server error fix (9d75919 )
similar organism display layout is altered (f033847 )
slug is corrected (ea90d4c )
small screen optimisation (27c2b9c )
specifying social card image height (8c39777 )
stream lined the form filed for molecules (f7f6b4a )
synonyms null check added (2792020 )
tailwind config preset missing bug fix (0535511 )
text area import issue fix (b1246e6 )
text search ordering added (0ebb9b9 )
the cache values are replaced with table columns filled using raw sql to improve performance (83f57fa )
the command is updated to handle organisms whose molecules have all been assigned to another organism (2a15149 )
the curation process now updates the molecule counts after the re-association of the molecules (b8f8369 )
to wrap the report tile in the table (a3da8b1 )
turned the molecule query into raw and added info messages (96369f7 )
two new commands for deduplicating the synonyms and updating the name with the first synonym where name is null (b1cad31 )
typos and docs update (53de6c8 )
undone few previous changes and fine tuned the DOI fetching and displaying the fields. (cc281d2 )
update citations README.md (98ddf2e )
update doi CITATION.cff (e9f6808 )
update release-please token (665e84c )
update to the fetch querry to avoid missing slugs (0907091 )
updated about page (3224bde )
updated about page, details page corrections and added missing data - NPAtlas import command (aa7417d )
updated CD link and release notes in download page (9806d5c )
updated collections schema and also typo correction (1716888 )
updated default collections filtering and ordering logic (0eab9a4 )
updated docs content (2fa76dc )
updated docs links (5f209e4 )
updated download links and other meta data (1ddc16b )
updated download page on coconut (383314d )
updated download page, removed bg pattern and other minor updates (68c7979 )
updated downloads (new release added) (8f0c484 )
updated favicon (221b67f )
updated header (84c3770 )
updated landing page with search and other options, minor query updates (f6d2402 )
updated links to report and request changes (edb02e2 )
updated meta tags (37b5cbb )
updated molecule card and added counts to the molecules table (4752a2e )
updated package lock (bacc8f5 )
updated search query (fd934d5 )
updated smiles search with sort order (beba591 )
updated the policies to allow user to create new reports and attach molecules, collections or citations to the report (017cf77 )
updated the search placeholder and about texts (583bc04 )
updated total molecules query (8f68374 )
updated twitter card (ba5ccab )
users with any role can now deactivate (49b2afa )
various docs updates (4e85abd )
various landing page optimisations (3f1bdcf )
various landing page updates, search sorting implementation and other minor updates (f0ead1b )
various minor updates (1dd36fb )
various updates (7f31573 )
various updates (c49023e )
view page is removed (dd14ff3 )
vitepress build updates (4b7f0e1 )
zenodo link introduction.md (0169c2b )
Miscellaneous Chores
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