chore(main): release 1.0.0

[Kohulan]

🤖 I have created a release beep boop

1.0.0 (2024-12-16)

Features

• a download option is provided for the respective mol files from CDK and RDKit (662cd84)
• a new script is now available to update the auto increment columns (13378b3)
• added all the available columns from molecules and properties tables to facilitate api search (f93caa5)
• added all the other properties plots to the stats page (15f44e3)
• added bioschema to molecule pages (3ccfdb2)
• added chembl name importer (8fa1c88)
• added copy to clipboard button (884fe74)
• added direct links to lens.org (resolves #2) (114503e)
• added feature to exclude collections (ce5c5af)
• added foreign key on structures table linking it to molecules table and added the relation in the models (fe580af)
• added list view (1341264)
• added meta_data column (82a3bd5)
• added new columns to sample location tables (00f7e68)
• added np_classifier in compound details and history ui updates (3c97f6b)
• added SDF download link to collection details page and ui bug fixes on data-sources views (4b2d56b)
• added SEO (34a62d9)
• added stats page and nplikeliness density plot (328410c)
• added the annotations plot to stats page (40f85d7)
• added transition for the show and hide history (0a707d4)
• added zoom and scroll features (3c2f446)
• altered the edit and view pages to load the new structure of the suggested changes (0f2acbe)
• altered the edit and view pages to load the new structure of the suggested changes (8f8113d)
• assign DOIs to collections (0d6acf3)
• assign identifiers to collections (ee60475)
• audits on the structures table are added to the timeline (a4109d8)
• basic density plot for overall nplikeness scores (38af621)
• ChEBI names importer is now available (6ecf269)
• clicking the classes takes to molecules search with that specific class (a2e2534)
• command to generate density plot json for all numeric columns of specified tables (e8316fa)
• command to generate frequency bubble chart data (0f7fc4c)
• compound time line is now available (b844ba8)
• Create bug_report.yml (5de141f)
• Create natural_products_submission.yml (8f1b74f)
• db schema is updated and now linked to info.coconut account (ae86e9f)
• download button for 3d molecules is now available (42c0274)
• enable local docker composer prod deployement (edb928b)
• enabled announcement banners (e084c22)
• enabled basic implementation of search (4dbede1)
• enabled create time pop-up modal to display overall changes being requested (97a11db)
• enabled create time pop-up modal to display overall changes being requested (2c1149f)
• enabled mol / sdf drag drop (fe0b4f6)
• extend Bioschemas metadata (11ce7ca)
• force https redirect and docker compose prod updates (6735e6d)
• franken php octane working docker image and compose file added (36fccfa)
• history of the compound is now available in the compound details page (bc26426)
• implemented organism local search (6f15492)
• improved suggestions by replacing the old key value pairs with tabs that can be approved by curators (49b918d)
• improved suggestions by replacing the old key value pairs with tabs that can be approved by curators (058d942)
• improved the user friendliness (wip) (1475c47)
• improved the user friendliness (wip) (8fef446)
• improved the user friendliness of the command using prompts (d405d60)
• install d3 package (4690313)
• interactive tooltip (b31ca20)
• molecule citation relation can now be searched by doi as well to attach citations to the molecule. (71645e5)
• 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)
• new bubble frequency chart and data (b57ee98)
• new column assinged_to is added to the reports table (0e3278b)
• new command to fix duplicates and missing links for the molecules pointing to the source datasets online. (efd4626)
• new command to import a set of jsons in a folder (be708bc)
• new command to import IUPAC names from Lexichem and fill in missing names (467d494)
• new command to import np classifier columns (3c3cb16)
• new command to import the 2d SDFs into structures table (1569b81)
• new docs (2b2e433)
• new helper functions and fixes to the old ones to accommodate report suggestions workflow. (ed645af)
• new helper functions and fixes to the old ones to accommodate report suggestions workflow. (bc36e7d)
• new interactive command to reassign molecules to a selected organism from the list of duplicates based on slug (7adb664)
• new issues relation for molecules is created (13539f3)
• new model and related migrations for issues table (f5f58d8)
• new pages added (4ecf171)
• new plot for annotation level (388e031)
• new route for charts (c58ec6d)
• new slug column is added to organisms table (2d268c3)
• now citations can be searched by doi from the report's molecule relation manager. (0726de4)
• now IUPAC names are displayed with proper italicisation. (c2d3c52)
• now only the fields requested for changes are available and the rest are disabled in edit page (206dc4b)
• now the search allows for partial inchikey search (10711c4)
• now the time line also shows audits from the properties table as well (b85f9d9)
• now timeline can handle citations (6c1c1aa)
• now timeline can handle citations (cceba8e)
• now users can skip a group of records and proceed to the next (af543ec)
• observer is created on molecule model to flush the model from cache after update (f56ef21)
• on hover now indicates which source the file is being downloaded from (46c3a16)
• original suggestions are saved and never touched, instead a separate copy is made available for curators to work on (9c2d3f3)
• prod build (925c2ec)
• python script for uploading collection wise sdfs (aa6db10)
• re-assignment of molecules functionality with audits is now available (824e06d)
• relation to retrieve the assigned user is added to the user model (2cabe52)
• 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)
• similar named organisms are displayed on the edit page of organisms with an option to edit them (36622d4)
• similarity based filters enabled (b3f04bb)
• the report changes form is made user friendly with pre-filled fields (f650aee)
• the report changes form is made user friendly with pre-filled fields (96b2dc8)
• updated october 2024 release (3e7733b)
• updated pagination logic and added loading screen while fetching results. fixes #220 (7fabdd4)
• users with any role can now see an additional filter tab assigned. The rest of the queries are scoped as per the access privileges. (21838e9)
• users with any roles can now assign reports for curation (6987ddf)

Bug Fixes

• 2d download is now fetched from the db (8ac4729)
• 3d rendering login updates, various other small updates (ed75cf0)
• access restrictions and improved user-friendliness (3826800)
• accessibility issues resolved and also enabled source maps (b9fad04)
• added another argument for giving base directory (2d66702)
• added cache policy for images and also updated links in application logo (87295ca)
• added coconut molecule search action back (ed5e8fe)
• added gzip compression (faf9c9c)
• added img alt text (96cd466)
• added IRI link to the organisms table (ff6df46)
• added matomo scripts to layout pages (2f051ad)
• added missing bcmath extension to php docker container (5a83108)
• added missing command (a0c8dd8)
• added missing libraries (20d6b23)
• added missing media drop (e10f109)
• added missing stats.php (38c6b45)
• added preview link to structure image (055e66b)
• added remove duplicates command (4bda2f8)
• added repository (d0652b3)
• added required libs (f46711e)
• added search history, collection url resolution bug fix, chemical classes issue fix (9d520a3)
• added styles and scripts to app (462affb)
• added support for old coconut urls (f7d8eed)
• added transparent favicon (163e683)
• added yes flag to install commands (2f53219)
• additional checks (c71fbc2)
• adjusted collection width on home page (d96e5a7)
• advanced search issue fix (b600bb8)
• advanced search pagination overlay bug fix and 503 title updates (7861c27)
• aligned the code as per the comment structure on molecule (34071b1)
• all the values caches are set to expire after 2 days. (847137f)
• altered the column names (4e7d11c)
• anchor with in anchor bug fix (45720f6)
• app name conflict issue fix (411916b)
• AttributeError: 'NoneType' object has no attribute 'people' fix (56433df)
• audit fix (2b3f5f5)
• auto flush removed for dash widgets and geo-locations' widgets get the data on the fly when the page is accessed. (9ad6641)
• broken classification links fix (5ba0554)
• bubble colours, chart size and queries. (24f3f25)
• bug fixes in schema and other updates to 3d rendering (ce4b9f9)
• build deployment (6d15b0d)
• bulk activate and de-activate is fixed (13a0997)
• ceph file system driver configured (88f6a0d)
• changed the column to is_resolved and added detach functions (5561b5d)
• classes are now made clickable which open corresponding searches in new tab (2d89b6b)
• collection image updates (ee160e9)
• collections image override bug fix and auditables relation manager bug fix (a35bb25)
• column altered to handle empty name (3b831eb)
• command is corrected and data regenerated (ebf016f)
• concatenating 0 to the cnp id (b32f65b)
• conditional checks were refined to work with the data structures of audits. (87363b3)
• conditional hidden issue fix (bf48f25)
• conditional toolkit rendering enabled on molecular 2d views (0d225bb)
• cookie consent privacy and terms of use links are pointed to the proper routes (c2c4b49)
• copy buttons now have a time out of 4 seconds to reset (335fdc2)
• correct name for the command (d67dd04)
• corrected the fillable arrays inline with production db (beadcb8)
• corrected the name and alignment (85feb5c)
• corrected the queries, handling datatypes and skipped collection wise stats for unnecessary columns (00b2d9a)
• corrections to the titles (0097c84)
• created indexes, added logic for handling integer columns, and corrected getDensityStats query. (e51ac48)
• css updates fix (a35eac3)
• curators can only see open reports in the assigned tab (ddde34b)
• database schema display (1795c15)
• default base dir is the current working directory (1ab3f9a)
• delete organisms with no molecules and enables audit trail (7ca9c65)
• deleted the old statement (31ddfb0)
• disabled filament backup plugin and docker deployment updates (762b366)
• disabled history show by default and header to represent the event (afa3037)
• disabled logging empty values and enabled handling of existing empty values in both old and new columns (f858ec0)
• disabled logging empty values and enabled handling of existing empty values in both old and new columns (bef6b8d)
• disabled rest authorisation cache (61ad3bc)
• displaying revoked molecule details on the web page (df336a9)
• docs logo fix and missing favicon.ico isse fix (6bd626f)
• DOI issue fixed (b03eae8)
• DOI issues fix (916cc60)
• download page css updates (104f17b)
• enabled ARG COMPOSER_AUTH (cb6411e)
• enabled auditing (7a88fbe)
• enabled cookie banner display on smaller screens (b6c4d6b)
• enabled DOI links on collection pages (a3b1b5f)
• enabled https redirect and also gzip compression (5c74027)
• enabled php redis (996baa4)
• fixed git ignore path for docs (eca6feb)
• fixed the audit relation manager error by flattening the old and new values (12c9e0e)
• fixed the file name issue (5893c54)
• fixes the array for the parents (1ba14ec)
• handles empty values in the old and new values of audits and displays the columns names in title case instead of the camel case (e2ecb4f)
• handles null values during approvals, fixes curator access issues and report approval errors (4f661a8)
• header issues resolved, tag line updates and other small bug fixes (644a319)
• hidden field issues are fixed (8d224dd)
• history time line of molecules is tuned to work with new custom audits (7c7fd3a)
• horizon gate updates (bec1e4c)
• imporved introduction and statistics (d07515e)
• 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)
• increased memory limit (aea897a)
• increased memory limit further for 2D structure import (e1b4881)
• introduced toggle buttons (583e295)
• key issue fixed (ceba3a9)
• key issue fixed (2da1fcf)
• layout updates on 2d rendering (ef0ecdc)
• legend scroll issue (e7e2624)
• links in the footer are now working (82fa0b9)
• list search is improved (643614f)
• 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)
• minor fix related to creating citations (b75caa4)
• minor fix related to creating citations (ff4621b)
• minor updates (2ce527d)
• missing collection name in social card bug fix (9f63111)
• missing identifiers now returns 404 and also added hasvariants logic to molecule details page (48c5a4d)
• more updates (852e227)
• more updates to header (535aa85)
• names in titles, axes and legends are corrected (8e84a70)
• nginx default config updates (667912a)
• 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 similar organisms list excludes the same organism name (1999287)
• now the time line shows synonym and cas changes properly (5a669cc)
• now the time line shows synonym and cas changes properly (716fe43)
• now the timestamps are auto managed for the pivot table molecule_sample_location (6396ce9)
• now the timestamps are auto managed for the pivot table molecule_sample_location (b6067a5)
• now whenever user is absent in the audit data, it gets filled with the coconut curator id (cf2788f)
• npm update (1e2c4f0)
• only assigned users now have access to edit view of reports (0c2af60)
• optimised the code with indexes and batches (48b6f8a)
• packages update (a544ec2)
• pagination dark mode css removed (40800c6)
• path issues fix (2f4d64e)
• php out of memory fix (0f1e02e)
• pointer alignment with curves (02e1388)
• reason from reports table is removed since there is a column comment that curators can use (37c1c50)
• recent molecules max width and mobile nav bar missing links added (50dda62)
• recent searches overflow scroll fix (0e89a30)
• redirect to view page after the report is approved (0ded278)
• Redis not found bug fix (392080f)
• refactored the form into the Citations model and applied a minor fix to creating citations. (efab97f)
• references to the compounds' source links are correctly parsed and displayed. (43b88f7)
• remove SSL config since its configured using GKE ingress (bbcaa49)
• removed cache flush from the coconut cache command (fa75c27)
• removed d3 imports (9fd9259)
• removed flush db command (ad22b40)
• removed python2 (56b0a45)
• removed python2 to resolve Package 'python2' has no installation candidate (668d489)
• removed rename (275330b)
• removed the toolkit as we are only using RDKit (c373d45)
• removed unnecessary d3 imports (e3b6c1a)
• replaced the or with and condition (885c2db)
• reset nginx conf (f47eac6)
• reset previous commits (ffea98a)
• resolved broken pagination links issue #305 (0ecb636)
• resolved dark mode (19c52c2)
• resolved npm issues (5fc491c)
• resolves #315 (f030da4)
• reverted docker compose build approach (9708ddd)
• reverted to pinging the api for now (a061a35)
• sail network issue (36b0139)
• sail network issue fix (74ab411)
• save modal is only displayed if it is a change (5670f31)
• saving doi for reporting (658ff2f)
• saving the overall suggested changes so that they are available in both the original and curator jsons (607535c)
• scrolling while zoomed in is fixed. (36fe92a)
• server error fix (9d75919)
• similar organism display layout is altered (f033847)
• slug is corrected (ea90d4c)
• sluggify only removes spaces and converts to lower case (3e1958d)
• small screen optimisation (27c2b9c)
• specifying social card image height (8c39777)
• 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)
• the disabling of non-suggested fields is restricted only to edit (7e83f7b)
• the missing molecules are excluded (905f092)
• the request now goes to rdkit instead of opedbabel which was throwing bad gateway error. (7e0fe0f)
• the status of the molecule now sets to revoked while deactivation (a275b02)
• to capture audits from citations (54bc73f)
• to handle italicised display of iupac name when name is not available (22187a3)
• to open reporting in a new tab (3f999a4)
• to wrap the report tile in the table (a3da8b1)
• typo (dbf6c0d)
• typo fixed (67dda8b)
• typos and docs update (53de6c8)
• update citations README.md (98ddf2e)
• update release-please token (665e84c)
• update to the fetch querry to avoid missing slugs (0907091)
• updated 503 maintenance mode error page (6943418)
• updated about page, details page corrections and added missing data - NPAtlas import command (aa7417d)
• updated action name and composer auth.json issue fix (19d2e36)
• updated CD link and release notes in download page (9806d5c)
• updated citation (67af50d)
• updated cm public api key and other minor updates (a63931c)
• updated coconut collection assign doi command updated (6fd1a71)
• updated collections schema and also typo correction (1716888)
• updated default collections filtering and ordering logic (0eab9a4)
• updated docker hub build action to new octane and other minor updates (9f633c9)
• updated docs content (2fa76dc)
• updated download links and other meta data (1ddc16b)
• updated download page on coconut (383314d)
• updated downloads (new release added) (8f0c484)
• updated gitignore file (2ecc218)
• updated header (84c3770)
• updated meta tags (37b5cbb)
• updated readme (73380ae)
• updated root folder (1cd3680)
• updated search query (fd934d5)
• updated total molecules query (8f68374)
• updated twitter card (ba5ccab)
• users can not edit the submitted reports and creation time null report record is handled. (ed4e0d1)
• various bug fixes (4e93b93)
• various fixes to handle null values and to hide the report/suggestion options altogether. (186d23c)
• various fixes to the reporting workflow (ca3dfdf)
• various landing page optimisations (3f1bdcf)
• various minor fixes (c74c046)
• various minor updates (1dd36fb)
• various updates (7f31573)
• vitepress build updates (4b7f0e1)
• which items received approval is now saved when approved, no need to save the form before approval (53847b0)

Miscellaneous Chores

• added documentation for 2D and 3D sdfs downloads (f856c51)
• added rest api, citation, updated the downloads image. (1b8df8f)
• code formatting updates (d3fb756)
• code optimisation (a77cb3d)
• commented out the slide over (wip) (51510be)
• commented out the slide over (wip) (d7dbc88)
• docs build (df06862)
• docs updates (6e7317c)
• docs vitepress build updates (cde6838)
• fix typo curation.md (e8207c1)
• formatting changes (10d3283)
• formatting changes (3ce816a)
• formatting changes (175d5fa)
• formatting changes (0aad094)
• formatting changes (e367a2e)
• formatting changes (ac74a75)
• formatting changes (de5433b)
• issue fix - added / (d9540c1)
• main: release 1.0.0 (bbd4474)
• new docs updates (cbb9124)
• pint updates (24f56cb)
• rearranged the look and descriptions of the download (e9947a3)
• refactored the code (0dc5535)
• removed cached ignore files (c12084a)
• removed dd statements. (0eb2497)
• removed dd statements. (ae4bd28)
• removed guides navigation link (d2c655d)
• removed old code (d32d114)
• removed the redundant sections (be78d5f)
• reorganised the conditions for efficiency (d318b52)
• update citation (4104e11)
• updated as per discussion with Chandu except audit history since it needs beautification (7cf08eb)
• updated readme (5d1e1a2)
• updated the command names to coconut namespace (d4147a2)
• updates to local and public instance documentation (38d9c4a)
• vitepress cache config conflicts fix (910a2e7)

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