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AGR curation release notes

https://agr-jira.atlassian.net/wiki/spaces/ATEAM/overview

v0.35.0

  • New features
    • Load FBcv into the persistent store (SCRUM-2190)
    • Implement Gene Type field/column for Genes data table (SCRUM-3983)
    • Turn off auxiliary clean up for associated entities (e.g. clean up of disease annotations based on a gene load) - public site Indexer work (SCRUM-4150)
    • SQTR Gene Associations import into Persistent store (SCRUM-4185, SCRUM-4187, SCRUM-4188)
    • HTPdataset loaded into persistent store (SCRUM-4192,SCRUM-4303, SCRUM-4341)
    • Make obsolete disease annotations hidden by default for all MOD default settings (SCRUM-4277)
    • HTPdataset ZFIN Fms files having wrong naming of property (SCRUM-4328)
    • Clean up erroneous DOTerms (SCRUM-4337)
    • Importing expression annotations into the persistent store - Load ExpressionPattern, TemporalContext, and AnatomicalSite (SCRUM-3952)
    • Implement programmatic, regular purging of exception message history for all exceptions older than 2 weeks (SCRUM-4377)
    • HTPdatasetSample import P1 - Creating entities and migration file (SCRUM-4426)
    • Reenable downloading of all exception messages for a given data load (SCRUM-4452)
    • P1: Expression Atlas Import: Load accession data files from Ensembl, etc... (SCRUM-4118)
    • GFF Loading (Load assembly, transcripts, exons, and CDSs without positional information; Load positional information for Transcripts, Exons, and CDSs; Load associations between Genes, Transcripts, Exons, and CDSs) (SCRUM-4174, SCRUM-4175, SCRUM-4176)
    • Associate Expression Annotations with Go Slim Terms (SCRUM-4300)
    • Implement caching of references for DQM loads (SCRUM-4336)
    • Accommodate BIOGRID-ORCS loader data type: to establish 3rd part link out to BIOGRID from gene page phenotypes section P1 - create DTO, load via migration, and loading infrastructure (SCRUM-4440)
    • Investigate: Accommodate BIOGRID-ORCS loader data type: to establish 3rd part link out to BIOGRID from gene page phenotypes section (SCRUM-4471)
    • Load VariantGenomicLocationAssociation from FMS submissions and generate HGVSg identifiers (SCRUM-4499)
    • Test effect of removing AuditedObject fields on disease annotation indexing speed (SCRUM-4520)
    • Java model changes for disease genetic modifier changes to split based on modifier type (SCRUM-4523)
    • Curation UI changes to Disease Annotations table to split out Genetic Modifiers into 3 separate fields for each of Gene, Allele and AGM modifier types (SCRUM-4524)
  • Fixes and maintenance
    • Edit cancelation button getting squeezed out of frame on alpha data tables (SCRUM-4236)
    • Constructs data table on alpha-curation throwing 500 error and not loading (SCRUM-4259)
    • Fix SQTR Gene Association Integration Tests (SCRUM-4299)
    • Curl timing out when uploading to persistent store (SCRUM-3683)
    • Annotations and interactions not indexed on alpha-curation (despite attempts to reindex) (SCRUM-4254)
    • Loads not showing in the Data Loads page "Data Processing Info Table" widget (SCRUM-4428)
    • New "Running Time" showing negative time counting down (SCRUM-4429)
    • Molecule table columns expand automatically when sorting (SCRUM-4531)

v0.34.0

  • New features
    • Paralogy annotations loaded into persistent store (SCRUM-4086, SCRUM-4088, SCRUM-4089, SCRUM-4090)
    • Expression annotations loaded into persistent store (SCRUM-3708)
    • HTPTags loaded into persistent store (SCRUM-4221)
    • Data load file history sorted by Load Started timestamp (SCRUM-4204)
    • Data loads stopped if error rate exceeds cutoff threshold (SCRUM-3871)
    • SGD strain background added to defining fields of disease/phenotype annotations (SCRUM-4137)
    • Turned off cleanup of associated annotations/associations (SCRUM-4107)
  • Fixes and maintenance
    • Fixed reporting of out-of-date errors in data loads tooltip (SCRUM-4210)
    • Fixed loading of genes with duplicate cross-references (SCRUM-4160)
    • Fixed lading of interactions via NCBI_Gene cross-references (SCRUM-4159)
    • Fixed orthology load cleanup (SCRUM-4146)
    • Fixed duplicate references on interactions (SCRUM-4114)
    • Fixed subject filter on disease annotations table (SCRUM-4113)
    • Fixed association of secondary phenotype annotations with primary annotations that have condition relations (SCRUM-4062)
    • Fixed downloads of large exception lists (SCRUM-3871)
    • Fixed missing exception messages in downloads (SCRUM-4162)

v0.33.0

  • New features
    • Importing gene interactions into the persistent store (phase 2) (SCRUM-3809)
    • Load SARS-CoV-2 genes into the persistent store (SCRUM-3929)
    • Remove apparently redundant subclass (e.g. Gene Disease Annotations) links from curation Dashboard (SCRUM-3954)
    • Hide obsolete rows (filter obsolete = false) when resetting the table to default settings (SCRUM-3960)
    • Reduce empty space in all remaining tables to create a more compact representation (SCRUM-3968)
  • Fixes and maintenance
    • Refactor Constructs Templates Table into Components (SCRUM-3755)
    • Refactor Genes Table Templates into Components (SCRUM-3759)
    • Refactor Literature Reference Table Templates into Components (SCRUM-3762)
    • Refactor useGenericDataTable's useQuery into a seperate useGetTableData hook (SCRUM-3803)
    • Upgrade to React 18 (SCRUM-3894)
    • Obsolete GO & CHEBI terms cluttering up root level Tree View (SCRUM-3918)
    • Fix interaction bulk load cleanup failures (SCRUM-3944)

v0.32.0

  • New features
    • Loading Gene phenotype annotations from the FMS (SCRUM-3686)
    • Loading Gene molecular interactions from the FMS - phase 1 (SCRUM-3806)
    • Lading Allele phenotype annotations from the FMS (SCRUM-3711)
    • Enable MOD-specific required fields for new disease annotations and editing existing annotations (SCRUM-2755)
    • GraphQL-like mechanism to trim unnecessary fields from API responses (SCRUM-3800)
    • Added functionality to OR filters in search
  • Fixes and maintenance
    • In search documentation
    • In display after clicking on save and add on the New annotation form
    • Change default number of rows rendered for each curation data table to 10 (SCRUM-3857)
    • Refactor Species Table Templates into Components (SCRUM-3765)
    • Refactor Allele Table Templates into Components (SCRUM-3753)
    • Vocabulary term lookup when creating experiments
    • Changed the mod related setting specifically to ZFIN
    • Changed the data tables items into alphabetical order
    • Increase reporting interval for bulk loads
    • Hardcode the RGD publication ID for OMIM and ORPHA ID cross references for Human gene phenotype annotations from the FMS(SCRUM-3883)
    • ATP:0000035 not showing up in ATP ontology Tree View (SCRUM-3884)

v0.31.0

  • New features
    • Replaced Negated column/field with NOT in disease annotation table and new annotation form (SCRUM-3794)
    • Enabled loading of AGM Phenotype Annotations from FMS (SCRUM-3712)
    • Added restrictions to Allele Gene Associations to prevent duplicate associations or multiple is_allele_of associations (SCRUM-3625 & SCRUM-3626)
    • Added GENO Ontology load (SCRUM-3694)
    • Establised persistence of new annotation pop-up field visibility settings for disease annotations (SCRUM-3661)
  • Fixes and maintenance
    • Aligned codebase with LinkML v2.2.0 (SCRUM-3515)
    • Fixed WB Molecular bulk load error (SCRUM-3823)
    • Added warning and provided openAPI definition download link on Swagger page (SCRUM-3779)
    • Automated cleanup of exception messages from old submissions (SCRUM-3795)
    • Removed unnecessary glyphs from ontology tree where no child terms (SCRUM-3249)
    • Improved speed of closure queries to address failing ontology loads (SCRUM-3780)
    • Improved speed of ID retrieval for data cleanup (SCRUM-3770)

v0.30.0

  • New features
    • Enable "New Annotation" pop-up field-visibility custom settings for disease annotations (SCRUM-2680)
    • Add and enable "Show All Fields" button for "New Annotation" pop-up for disease annotations (SCRUM-2756)
  • Fixes and maintenance
    • Address deletion of allele-gene associations on the Allele detail page Allele-Gene Associations table (SCRUM-3637)
    • ZFIN Allele load mostly failing with apparent unrecognized PMID not present in most cases (SCRUM-3640)
    • Duplicate disease annotations (same Unique ID) on production curation (SCRUM-3641)

v0.29.0

  • New features

    • Allele detail page: Visually emphasize field names/sections and visually demphasize 'Add' buttons (SCRUM-3343)
    • Report Failed Loads table in Data Loads page UI (SCRUM-3440)
    • Notify developers via Slack of failed curation system loads (SCRUM-3470)
    • Provide "Saving in progress" indicator and inactivate interaction with page on allele detail pages (SCRUM-3536)
    • Move "Add" buttons in Allele detail page to right of field names (in-line)(SCRUM-3551)
    • Reduce empty space in disease annotations table to create a more compact representation (SCRUM-3564)
    • Enable downloading of all exception messages for a given data load (SCRUM-2639)

  • Fixes and maintenance

    • Upgrade python version used in agr_db_backups (SCRUM-3094)
    • FB constructs failing to load (SCRUM-3613)
    • Fix failing Construct Association loads (SCRUM-3620)
    • SGD Allele load failing with uninterpretable exception messages (SCRUM-3630)
    • Attempting to display FB constructs with secondary IDs in Constructs table (on alpha) throws error (SCRUM-3631)
    • RGD Allele load entries failing incorrectly (SCRUM-3633)
    • Create Json View to Limit data from Disease Annotations (SCRUM-3588)

v0.28.0-rc2

  • Updates quarkus to version 3
  • Fixes and maintenance

v0.27.2 & v0.27.3

  • Fixes and maintenance
    • Fixes for permissions and dependent workflow triggering on automated release creation (SCRUM-3444)

v0.27.1

  • Fixes and maintenance
    • Automated release creation (SCRUM-3444)
    • Added branch-tagging to latest beta and production container images (SCRUM-3415)
    • Updated SSL Cert to Auto-renewed Amazon-issued Certificate

v0.27.0

  • New features
    • Allele details page changes:
      • Enabled display and editing of Nomenclature Events of alleles on allele details page (SCRUM-3345)
      • Enabled load and display of Allele-Gene associations on allele details page (SCRUM-2248)
      • Moved allele detail page references into table (SCRUM-3353)
    • Enabled load and display of variant table (SCRUM-3321)
    • Enabled load and display of ConstructGenomicEntityAssociation (construct table) (SCRUM-3325)
  • Fixes and maintenance
    • Clean up and consolidate vocabularies into sets (SCRUM-3322)
    • Fixed dropdown selection registration bug (SCRUM-3357)
    • Added association classes to linkML Schema Version Table reporting compatible LinkML versions
    • Prevent duplicates in multi-select autocomplete (SCRUM-3387)

v0.26.0

  • New features
    • Improved healthcheck endpoints and added health page (#1228 and #1230)
    • Added FMS Data Files page (#1247)
    • Enabled display and editing of Name property of alleles on Allele Detail pages (SCRUM-3124)
    • Expanded allele nomenclature events pop-up display to include created/updated AuditedObject properties (SCRUM-3220)
    • Enabled display and editing of Mutation Type property of alleles on Allele Detail pages (SCRUM-3128)
    • Enabled load and display of constructs (SCRUM-199)
    • Enabled display and editing of ... of alleles on allele details page:
      • Inheritance Modes (SCRUM-3132)
      • Secondary IDs (SCRUM-3127)
      • Database Status (SCRUM-3131)
      • Related Notes (SCRUM-3133)
      • Functional Impacts (SCRUM-3129)
      • Sumbol (SCRUM-3125)
      • GermlineTransmissionStatus (SCRUM-3130)
    • Display crossReferences in table on allele detail page (SCRUM-3200)
    • Display MOD release version on DataLoads page (SCRUM-3336)
  • Fixes and maintenance
    • Fixed drop down selection bug on Allele Detail page (SCRUM-3316)
    • Increase readibility of experimental conditions in editing interfaces (SCRUM-3027)
    • Fixed error on saving row in Experiments table (SCRUM-3290)
    • Fix failing WB Molecule loads (SCRUM-3337)
    • ConditionRelation and ExperimentalCondition cleanup (SCRUM-3306)
    • Display next future (a.k.a current stage) release as default by @markquintontulloch (SCRUM-3268)
    • Update to align datamodels with LinkML v1.9.0 (SCRUM-3278)
    • Quarkus update for security fixes (SCRUM-3303)

v0.25.0

  • New features
    • Display and editing of allele synonyms on allele detail page (SCRUM-3126)
    • Keep the ontology browser term information panel in view while browsing the (SCRUM-3250)
    • Display uniqueId error message in row edit mode of Disease Annotations table (SCRUM-3248)
    • Display validation errors of hidden fields in row edit mode (SCRUM-3255)
    • Enable access to curation API using admin tokens without Okta user (SCRUM-3078)
    • Enable sorting of references by primary xref (SCRUM-2725)
  • Fixes and maintenance
    • Update curation system to align with LinkML v1.8.0 (SCRUM-3156)
    • Fix short citation display, sorting, and filtering in Literature References table (SCRUM-3247)

v0.24.0

  • New features

    • Load and display Allele 'allele_nomenclature_events' attribute (SCRUM-2340)
    • Restore gene page disease table Source column linkouts based on cross references and persistent store data (SCRUM-2372)
    • Show reference short citation in Disease Annotations table "New Annotation" pop-up human-readable values (SCRUM-2784)
    • Disallow entry of duplicate notes (SCRUM-3080)
    • Update Alliance gene page disease table download file to include primary annotation disease relation (SCRUM-3091)
    • Add primary disease annotation disease relation to the gene page disease table Annotation Details pop-up (SCRUM-3092)
    • Update species order of disease annotation display on gene pages (SCRUM-3093)
    • Enable display of read-only allele properties on Allele Detail page (SCRUM-3120)
    • Display allele symbol and curie at top of Allele Detail Page (SCRUM-3198)
    • Display species/taxon name next to Taxon data entry field on Allele Detail Page (SCRUM-3199)
    • Collapse redundant Based On entries on gene page disease tables (SCRUM-3201)

  • Fixes and maintenance

    • agr_mati GH-actions authentication credentials cleanup (SCRUM-3211)
    • Update agr_mati GH-actions authentication to AWS (SCRUM-3210)
    • Fix display of strain disease genetic modifier to display strain name instead of curie (SCRUM-3203)
    • Need to regenerate disease annotation Unique IDs on production Postgres according to new consensus set of defining properties (SCRUM-3190)
    • Release and deploy SCRUM-3143 fix to beta (as v0.22.0-rc2) (SCRUM-3144)
    • New Taxons not showing up after they are loaded (SCRUM-3169)
    • Ensure submitted data meets expectations for cleanup code parameters (SCRUM-3172)
    • Update agr_curation GH-actions authentication to AWS to prevent usage of long-lived secrets (SCRUM-3068)
    • cln-3.1 WB gene page disease annotations should be consolidated (SCRUM-2933)

v0.23.0

  • New features

    • "Vocabulary Label" field added to vocabularies and vocabulary term sets (SCRUM-3167)
    • Created Allele Detail page (SCRUM-3009)
    • Enabled display and editing of simple properties on Allele Detail page (SCRUM-3121)
    • Display short citation in human-readable values of reference field (SCRUM-2784)

  • Fixes and maintenance

    • Fixed display of load status in summary row (SCRUM-3117)
    • Fixed reporting of load failures due to invalid URL (SCRUM-2248)

v0.22.0

  • New features

    • Loaded orthology data (SCRUM-2710)
    • Loaded Xenbase genes and orthology data (SCRUM-3056)
    • Loaded Biological Spatial Ontology (BSPO) (SCRUM-3062)
    • Loaded Cell Ontology(CL) (SCRUM-3059)
    • Loaded Clinical Measurement Ontology (SCRUM-3060)
    • Loaded Pathway Ontology (PW) (SCRUM-3057)
    • Loaded Uberson Ontology (SCRUM-2454)
    • Loaded Rat Strain Ontology (RS) (SCRUM-3050)
    • Loaded Molecular Interactions Ontology (MI) (SCRUM-2451)
    • Loaded Mouse Pathology Ontology (MPATH) (SCRUM-2452)
    • Loaded Rat Strain Ontology (RS) (SCRUM-3036)

  • Fixes and maintenance

    • Bulk load cleanup procedure fixed (SCRUM-3143 & SCRUM-3073)
    • Removed DataProvider reset endpoint (SCRUM-3037)
    • Fixed age error when cancelling edit mode after having duplicated annotation (SCRUM-3030)
    • Fixed disappearing loads in Data Loads page when multiple loads running (SCRUM-3051)
    • Disabled reset buttons during row editing (SCRUM-3030)

v0.21.0

  • New features
    • Duplicate Disease Annotation popup (SCRUM-2911)
    • Updated display of ontology terms in Tree View (SCRUM-3021)
    • Improved display of notes popups (SCRUM-3005)
    • Switch to single consensus set of defining properties for disease annotations (SCRUM-3008)
    • Loaded Vertebrate Trait (VT) Ontology (SCRUM-2453)
    • Loaded Ascomycete Phenotype Ontology (APO) (SCRUM-2447)
    • Loaded Measurement Method Ontology (MMO) (SCRUM-1206)
    • Added Data Provider column to Alleles table (SCRUM-3006)
    • Added Data Provider column to Genes and AGMs tables (SCRUM-3007)
    • Prevented loading of duplicate notes (SCRUM-2828)
  • Fixes and maintenance
    • Allele indexing optimizations (SCRUM-2982)

v0.20.1

  • Fixes
    • Temporary endpoint to reset data provider on all disease annotations (SCRUM-3037)

v0.20.0

  • New features

    • Modify curation data submission API endpoint to include a "no clean up" option boolean (SCRUM-2932)
    • Load and display Allele 'allele_germline_transmission_status' attribute (SCRUM-2333)
    • Load and display Allele 'allele_functional_impacts' attribute (SCRUM-2334)
    • Load and display Allele 'related_notes' attribute (SCRUM-2341)
    • Expand gene page disease table "Annotation Details" pop-up to include all persistent store disease annotation information (SCRUM-2394)

  • Fixes & maintenance

    • Enable filtering on non-PMID references of disease annotations on gene pages (SCRUM-2727)
    • Upgrade machine size for the FMS to allow Paralogy work to continue (SCRUM-2848)
    • Add mock data for all data table tests (SCRUM-2900)
    • Upgrade quarkus to 3.0.3.Final (SCRUM-2908S)
    • Address outstanding slow Cacher query after Neo4J upgrade to version 5.5 (SCRUM-2909)
    • Fix broken public site API as a result of the Neo4J upgrade (SCRUM-2913)
    • Audit allele indexes on the database (SCRUM-2923)
    • UI miss-handling of cross references is breaking the disease annotations section in the main site (SCRUM-2925)

v0.19.1

  • Fixes
    • Fix cleanup of biological entities associated with disease annotation genetic modifiers (SCRUM-2918)
    • Fix duplication of slot annotations on reload of bulk file (SCRUM-2949)

v0.19.0

  • New features
    • Synchronizes to LinkML v1.7.1 release (SCRUM-2836)
    • Enable specification of object type in pending edit tooltip (SCRUM-2891)
    • Loading of gene secondary IDs and display of gene slot annotation fields (SCRUM-2800)
    • Sort out display/format text in UI code (SCRUM-2890)
    • Display and enable editing of allele synonyms (SCRUM-2342)
    • added HP Ontology (SCRUM-2449)
  • Fixes & maintenance
    • Remove deprecated secondaryId index references (SCRUM-2841)
    • Added basic component tests to most data tables (SCRUM-2877)
    • Fix table name (SCRUM-2342)
    • Remove legacy secondary IDs (SCRUM-2841)
    • Fix geneticModifiers autocomplete (SCRUM-28236)
    • Fix popup dialog autocomplete selection bug (SCRUM-2885)
    • updated row index for Autocomplete editors (SCRUM-2838)
    • Fix gene table tooltips (SCRUM-2870)
    • Fixed row cancel error (SCRUM-2838)
    • Fixed tooltip superscripts on GenesTable (SCRUM-2773)
    • Migration to populate null data providers (SCRUM-2830)

v0.18.0

  • New features
    • Rearrange "New Annotation" pop-up fields for disease annotations (SCRUM-2754)
    • Re-enable editing of allele symbol and name (SCRUM-2383)
    • Load Phenotype and Trait Ontology (PATO) into the persistent store (SCRUM-2450)
    • Load Human Phenotype Ontology (HP) into the persistent store (SCRUM-2449)
  • Fixes & maintenance
    • Fix some table state persistence bugs (SCRUM-2754)
    • Fix column reordering persistence (SCRUM-2457)
    • Fix Gene names being displayed in symbol field (SCRUM-2840)

v0.17.0

  • New features
    • Improved reporting of bulk load deprecation events (SCRUM-2761)
    • Implemented error boundaries for better error handling in UI (SCRUM-2587)
    • Prevented loading of annotations referencing ECOTerms not in AGR subset (SCRUM-2748)
    • Enabled loading of biological entities with non-canonical species (SCRUM-2679)
    • Enabled filtering of experimental conditions by relation type in disease annotation table (SCRUM-2718)
    • Improved filtering of evidence codes (SCRUM-189)
    • Implemented autopopulated dataProvider field for biological entities (SCRUM-2711)
    • Improved error reporting for post-load processing of data load files (SCRUM-2455)
    • Implemented multi-select picklist for data provider in diseaes annotations table (SCRUM-2509)
    • Enabled users to delete local storage entries in their profile page (SCRUM-2654)
    • Implemented first non-trivial tests in UI testing framework (SCRUM-2282)
    • Loaded WBPhenotype ontology (SCRUM-2446)
    • Prevented loading of data files formatted to unsupported LinkML schema versions (SCRUM-2627)
    • Implemented consistent ordering of data loads (SCRUM-2593)
    • Enabled deletion of disease annotations from persistent store with appropriate constraints (SCRUM-1907)
  • Fixes & maintenance
    • Rendering of boolean filter selections after table reset bug fixed (SCRUM-2757)
    • Rendering of gene name and symbol superscripts fixed (SCRUM-2678)
    • Forced selection from dropdown for biological entity fields (SCRUM-2698)
    • Implemented cleanup of non-submitted ingest sets in data loads (SCRUM-2696)
    • Created centralised store for sort and filter fields for each table (SCRUM-2650)
    • Fixed indexing of slot annotation fields upon insert (SCRUM-2658)
    • Added check for valid fields in users' local storage (SCRUM-2526)
    • Added integration tests for creation of objects with only required fields (SCRUM-2601)
    • Fixed data loads exception popup refresh when no exceptions present (SCRUM-2594)

v0.16.0

  • New features
    • Prevent loading of biological entries from non-canonical species (SCRUM-2477)
    • Added Load Resource Descriptors file as load (SCRUM-2459)
    • Updated subject search ordering (#879)
  • Data updates
    • Updated FlyBase DiseaseAnnotation uniqueId fields to better capture unique entities (SCRUM-2503)
  • Maintenance
    • Tackle gh-actions deprecation warnings #881
    • enabled scheduled reindexing (SCRUM-2466)
  • Bugfixes:
    • SCRUM-2493 Filters issue on click og Rest to MOD button solved by @kthorat-prog in #883

v0.14.0

  • New features
    • Added confirmation popup to data loads widget upload file UI functionality
    • Exclude obsolete results from AutoComplete suggestions (except reference field) (SCRUM-2327)
    • Enabled deprecation (instead of deletion) of public disease annotations (1st iteration, SCRUM-2296 & SCRUM-2298)
    • Added alliance member affiliation (#808)
    • Display human-readable subject name underneath subject field (#816)
  • Data changes
    • Synchronised codebase with LinkML v1.5.0 (NameSlotAnnotations) (SCRUM-2311, SCRUM-2345)
  • Bug fixes
    • Fixed disabled filter after validation fail in Allele table (SCRUM-2326)
  • Maintenance
    • Upgrade quarkus to 2.14.2 (SCRUM-2330)

v0.13.0

  • New Features
    • Added 'Mutation types' to Allele table (SCRUM-2267 & SCRUM-2268)
    • Added 'Asserted Genes' and 'Asserted allele' fields to form for new disease annotations (SCRUM-2167)
    • Added Upload button for UI submission of bulk upload files (SCRUM-2092)
    • Added initial UI automated tests (SCRUM-1737)
    • Included invalid entity in bulk upload error message (SCRUM-2314)
    • Replaced Allele 'In Collection' dropdown menus with text search / Autocomplete editor (SCRUM-2293 & SCRUM-2295)
    • Synchronised codebase with LinkML v1.4.0 (SCRUM-2266)
    • Populated new Vocabulary form with default value for 'obsolete' field (SCRUM-2301
    • Sorted Vocabularies by name in editor dropdown (SCRUM-2302)
  • Fixes & maintenance
    • Autocomplete code refactored (SCRUM-2059)
    • Updated Github actions (SCRUM-2269)
    • Added check for Autocomplete selection on biological entity fields (SCRUM-2252)
    • Implemented handling of unexpected API errors upon saving entries in UI (SCRUM-2251)

v0.12.0

  • New Features
    • New service to call MaTI (SCRUM-2011)
    • Removed extra SiteLayout from routes (SCRUM-2160)
    • Renaming of Experiments table and column (SCRUM-2069, SCRUM-2070)
    • Refactor DTO validation code (SCRUM-2145)
    • Return exact matches only from dropdown filters (SCRUM-2139)
    • Make allele attributes editable (SCRUM-2161)
    • Add LinkML version submission documentation
    • Experiments dropdown to NewAnnotationForm (SCRUM-1917)
    • Enable entering identifiers of experimental condition components in autocomplete (SCRUM-2099)
  • Fixes
    • Fix for OR on multiselect fields
    • Fix synonym and reference persistence
    • Bug fixes and integration tests for updates with null value ( SCRUM-2174)
    • Fix reference autosuggest (SCRUM-2161)
    • Fix blank screen on ref deletion (SCRUM-2161)
    • Delete existing notes when doing DA bulk upload
    • Added indexes to allele touching tables

v0.11.0

  • New Features
    • Enable creation of disease annotation; 1st & 2nd iteration pop-up (SCRUM-1709, SCRUM-1903)
    • Enabled simple deletion of disease annotations (SCRUM-1890)
    • Condition Summaries & Unique IDs for Experimental Conditions (plan to retire Condition Statements)
      • Generate consistent condition_summary entries for experimental conditions (SCRUM-2036)
      • Generate consistent unique_id values for experimental conditions (SCRUM-2037)
      • Clean up experimental conditions (redundant entries + usage of condition_summary in place of condition_statement) (SCRUM-2038)
      • Add tooltip to condition autosuggest options to display unique_id values for each experimental condition displayed (SCRUM-2040)
      • Replace experimental condition autosuggest display with condition_summary instead of condition_statement (SCRUM-2039)
    • Add display of compatible LinkML schema versions (SCRUM-2091)
  • Fixes
    • Fix broken autocomplete for experimental conditions (SCRUM-2089)
    • Fix sort order of data loads by reverse chronological order (SCRUM-2010)
    • Fix missing ontologies from dashboard (SCRUM-2076)
    • Fix blank screen bug in Data Loads widget (SCRUM-2042)
    • Clean up and address stale file loads in Data Loads widget (SCRUM-2004)

v0.10.0

  • New features
    • Enabled disease annotation deletion (through UI) (SCRUM-1890)
    • Enabled disease annotation creation (through UI) (SCRUM-1709)
  • Data and schema changes
    • Synchronised curation application data model with LinkML schema v1.2.4 (SCRUM-1926)
  • Bugfixes, minor enhancements & maintenance
    • Enabled preventing disease-annotation save without reference/subject/object (SCRUM-1916)
    • Added additional integration tests for required fields (SCRUM-1939)
    • Minor indexing improvements (for the index everything endpoint)
    • Minor deployment notification fixes
    • Updated data validation to treat empty strings as empty values (SCRUM-1942)
    • Updated bulk load to correctly new null values on update (SCRUM-1975)
    • Fixed bulk load last loaded date (SCRUM-2000)
    • Cleanup of inconsistent records in DB (SCRUM-2005)
    • Fixed experimentalConditions UI filter (SCRUM-2003)
    • Fixed file sorting in data loads widget (SCRUM-2010)
    • Added additional note reference validation (SCRUM-2028)

v0.9.0

  • New features

    • Enabled deletion of relations in Condition Relation table (SCRUM-1605)
    • Enabled creation of Experimental Conditions (SCRUM-1848, SCRUM-1849, SCRUM-1850)
    • Added ATP ontology (SCRUM-1840)
    • Automatic population of createdBy field when creating new entries (SCRUM-1868)
    • Repurposed Condition Relation Handles table for all Condition Relations, with or without handle (SCRUM-1867)
    • Enabled deletion of controlled vocabulary terms (SCRUM-1889)
    • Added parents, ancestors, and closure to ontologies
    • Enabled per-class reporting of LinkML schema version compatibility

  • Bugfixes, minor enhancements & maintenance

    • API updates to enable deletion of disease annotations (SCRUM-1711)
    • Improved filter functionality for Experiments and Experimental Conditions columns in Disease Annotation table (SCRUM-1816)

v0.8.0

  • New features
    • Enabled ConditionRelation creation for disease annotation (SCRUM-1405)
    • Enabled dissociation of ConditionRelation from DiseaseAnnotation (SCRUM-1563)
    • Added inferred/asserted genes/aleles (SCRUM-1795, SCRUM-1796, SCRUM-1797)
    • Enabled AGM creation (for integration into ZFIN workflow) SCRUM-1724
    • Enabled deletion of experimental conditions (SCRUM-1799)
  • Bugfixes, minor enhancements & maintenance
    • Fixed argument display single type indexing endpoints (#571)
    • Fix activation of Keep Edits button on adding a note to disease annotation (SCRUM-1808)
    • Fixed experiment dropdown update reset on cancel (SCRUM-1806)
    • Append newly created condition relation handles to the top of the table (SCRUM-1801)
    • Switched search indexing from ElasticSearch to OpenSearch (SCRUM-1646, SCRUM-1647, SCRUM-1648)

v0.7.0

  • New Features
    • SCRUM-1743 new Vocabularies Table by @adamgibs in #566
    • SCRUM-1555 Make existing disease annotation ‘condition relations’ editable (no handle in use) by @markquintontulloch in #554
    • SCRUM-1556 Enable display and editing of existing disease annotation experiment handles by @markquintontulloch in #563
    • SCRUM-1765 Bring functionality of editing of 'related notes' in Disease Annotation table in line with that of 'condition relations' by @markquintontulloch in #559
  • Maintenance
    • SCRUM-1712 Synchronisation of References with Literature System by @markquintontulloch in #552, #557, #561, #564
    • SCRUM-1732 Fixed validation of references in conditionRelations #560
    • SCRUM-1710 Fixed multiple tooltips bug by @markquintontulloch in #565
    • SCRUM-1722 Fixed multi-line cell warnings bug by @adamgibs in #562
    • Added indexing params to reindexing endpoints by @mluypaert in #555
    • SCRUM-1676 Refactor of AutocompleteEditor template by @adamgibs in #547 SCRUM-1756 Fixed saving of notes attached to disease annotations bug by @markquintontulloch in #553

v0.6.0

  • New Features
    • SCRUM-1537 make condition relation handle table editable by @cmpich in #491
    • SCRUM-1537 validate null handle, disallow same handle/pub combination by @cmpich in #511
    • SCRUM-1537 add auto-complete on reference column on condition-relation-handle-table by @cmpich in #518
    • Filters icon added to Genric Data Table Component by @kthorat-prog in #505
    • Filters Label added on Roweditor frozen column by @kthorat-prog in #513
    • Obsolete Column added to disease annotations table by @kthorat-prog in #514
  • Data Load
    • SCRUM-1609, SCRUM-1611, SCRUM-1612 Loading and testing of obsolete field by @markquintontulloch in #503
  • Maintenance
    • Misc refactors by @adamgibs in #504
    • Column header names changed for 2 columns by @kthorat-prog in #508
    • SCRUM-1603 added VocabularyTermUpdate view to return vocabulary field by @adamgibs in #510
    • SCRUM-1598 Added DiseaseAnnotationUpdate view to conditions by @adamgibs in #512
    • null check added to col variable in useEffect by @kthorat-prog in #517
    • fixed autocomplete hover bug by @adamgibs in #520
    • SCRUM-516 SCRUM 1537 create getEntityType() method to select and display the auto-complete list, auto-complete for DA table by @cmpich in #519
    • SCRUM-1675 added check for conditions with no handle or reference by @adamgibs in #521

v0.4.0

  • Data loading
    • SCRUM-1205 Anatomy stage ontologies by @markquintontulloch in #3117
    • SCRUM-1319 Add AuditedObject fields to disease annotations by @markquintontulloch in #314
    • SCRUM-1205 MmusDv load update by @markquintontulloch in #324
    • SCRUM-737 update - SGD strain background filter by @markquintontulloch in #327
    • SCRUM-1298 Validate uniqueId doesn't exist after editing experimentalCondition by @markquintontulloch in #344
    • SCRUM-731 disease qualifiers by @markquintontulloch in #338
    • SCRUM-1326 Add condition summary to experimental conditions by @markquintontulloch in #352
    • SCRUM-1155 Limit ZECO terms for conditionClass to AGR SLIM by @markquintontulloch in #355
    • SCRUM-1369 Hide Parental Populations column in AGM table by default by @markquintontulloch in #353
    • Make ExperimentalCondition uniqueId generation consistent by @markquintontulloch in #360
    • SCRUM-1427 Submission of notes with disease annotations by @markquintontulloch in #392
    • SCRUM-1435 Backend code for conditionRelation editing via diseaseAnnotation edits by @markquintontulloch in #401
    • fix AGM creation logic by @cmpich in #370
    • SCRUM-1232 - Add Xenopus ontologies by @markquintontulloch in #424
    • SCRUM-1232 Enable multiple ontology loads from single OWL file by @markquintontulloch in #425
    • SCRUM-1232 Add additional namespace for XBA load by @markquintontulloch in #428
  • UI Features
    • UI reskin by @adamgibs in #305, #321, #334
    • Editor Refactor by @adamgibs in #309
    • Header freeze added by @kthorat-prog in #340
    • Added log server to list of other links by @oblodgett in #317
    • Changed button to use primreact styles by @oblodgett in #339
    • Changed links to open in a new tab by @oblodgett in #341
    • Template made for all datatables across website by @kthorat-prog in #357
    • SCRUM-1318 added filter field for condition relations handle by @adamgibs in #380
    • Added ellipsis & Tooltips for title,abstract & citation columns in Literature Ref Table by @kthorat-prog in #384
    • SCRUM-1403 Autopopulate 'Modified By' field on editing by @markquintontulloch in #381
    • Date modified and Modified fields are updated immediately on success by @kthorat-prog in #399
    • Generic data assignment done for immediate row update & Frozen Column removed by @kthorat-prog in #400
    • Edit Column is frozen and positioned to extreme left side of table by @kthorat-prog in #419
    • Dashboard list of table names sorted alphabetically for both tables by @kthorat-prog in #369
    • Literature Reference added to Dashboard & its Layout is changed to ma… by @kthorat-prog in #374
    • SCRUM-1426 display handle instead of conditions if available by @cmpich in #391
  • UI Maintenance
    • Remove columns with work still to do on UI by @markquintontulloch in #332
    • The ID column made non-sortable by @kthorat-prog in #331
    • SCRUM-737 Disable sgdStrainBackground editing for non-gene annotations by @markquintontulloch in #337
    • reduced DATable width by @adamgibs in #342
    • SCRUM-1368 turned filtering for AGM table name column back on by @adamgibs in #358
    • SCRUM-734 Fix spelling mistake by @markquintontulloch in #366
    • Misc refactor items by @adamgibs in #368
    • Header backgroundcolor added to make it opaque by @kthorat-prog in #376
    • SCRUM-1393 added default column order state to DA table by @adamgibs in #372
    • Changed dialog width, refactored list and changed dialog title by @adamgibs in #375
    • To make the error message float above the cell width for visibility by @kthorat-prog in #383
    • Taxon_ID column display changed and sort order is based on name now by @kthorat-prog in #394
    • Taxon display changed by @kthorat-prog in #398
    • SCRUM-1423 Changes done by Olin only by @kthorat-prog in #405
  • API Feature
    • SCRUM-1435 Add validation endpoint by @markquintontulloch in #402
    • SCRUM-1391 non-loaded allele removal by @mluypaert in #411
    • Added code for integration with Literature Reference ES Server by @oblodgett in #359
    • SCRUM-1371 + SCRUM-1396: non-loaded gene and agm removal by @mluypaert in #436
  • API Maintenance
    • SCRUM-1364 Add field name to response by @markquintontulloch in #350
    • SCRUM-1412 Fix inconsistency in inchiKey field naming by @markquintontulloch in #377
    • SCRUM-734 property bridge fix by @markquintontulloch in #363
    • Fixed params for tracking number of results by @oblodgett in #365
    • Use .keyword field for searching in the ABC SCRUM-1400 by @oblodgett in #367
    • Removed logging verbosity for loads by @oblodgett in #395
    • Updated ordering by @oblodgett in #397
    • Added comment for upcoming sprint (MERGE AFTER REVIEW) by @oblodgett in #416
    • Added stopped loads to be started (MERGE AFTER REVIEW) by @oblodgett in #417
    • paper handle fixes: index definition by @cmpich in #373
    • SCRUM-1318 handle condition updates, include handle info in unique ID by @cmpich in #385
    • SCRUM-1415 Set UniqueID for new ExperimentalCondition entities by @markquintontulloch in #386
    • Changed exception so they will print in the logs by @oblodgett in #430
    • SCRUM-1499 Improve error reporting for ConditionRelations and RelatedNotes attached to DAs by @markquintontulloch in #433
  • Other
    • Add MIT LICENSE file by @chris-grove in #421
    • Removed duplicate code PR into PR by @oblodgett in #426
    • SCRUM-1432 VocabularyTerm validation and integration tests by @markquintontulloch in #396
    • SCRUM-1279 by @markquintontulloch in #307
    • Scrum 1020 by @kthorat-prog in #319
    • SCRUM-1320 Switching of disease annotation enums to VocabularyTerms by @markquintontulloch in #318
    • Scrum 1296 by @adamgibs in #326
    • Switch vocabularyTerm lookup from search to find by @markquintontulloch in #328
    • SCRUM-1317 by @markquintontulloch in #346
    • Scrum 1341 by @adamgibs in #361
    • SCRUM-1318 by @adamgibs in #362
    • SCRUM-1393 by @adamgibs in #378
    • SCRUM-1394 by @adamgibs in #371
    • Scrum 1377a by @cmpich in #364
    • SCRUM-1315 by @adamgibs in #410
    • SCRUM-1401 by @adamgibs in #412
    • SCRUM-1315 by @adamgibs in #413
    • SCRUM-1401 by @adamgibs in #390
  • DevOps
    • SCRUM-1366 merge from beta to alpha by @markquintontulloch in #351
    • Merge v0.3.0-rc3 changes back into alpha by @mluypaert in #356
    • Merge-back production to beta after v0.3.0 release creation by @mluypaert in #404
    • SCRUM-1417: Release/v0.4.0-rc1 by @mluypaert in #407
    • Alpha deployment trigger update proposal by @mluypaert in #418
    • Release/v0.4.0 rc2 by @oblodgett in #423
    • PR merge/beta by @oblodgett in #432
    • Release/v0.4.0 rc4 by @kthorat-prog in #442
    • Release/v0.4.0 by @kthorat-prog in #446
    • SCRUM-1424 Renamed migration files to clear patch release version number by @mluypaert in #389
  • Bugs
    • Fixed API Token Login by @oblodgett in #313
    • Fixed status' on startup by @oblodgett in #315
    • Fixed obsolete on vocabulary pages by @oblodgett in #316
    • Fixed disease relation validation by @oblodgett in #320
    • Vocab UI fix by @markquintontulloch in #323
    • The changes to reflect in table as new term/vocab added is added. by @kthorat-prog in #330
    • Fix 'Cannot convert undefined or null to object' error by @markquintontulloch in #333
    • SCRUM-1205 fix for missing term by @markquintontulloch in #335
    • ControlledVocabularyDropdown fixes by @markquintontulloch in #336
    • SCRUM-1306 fixed synonyms bug for subject and with fields by @adamgibs in #343
    • SCRUM-1360 fixed dropdown refocus bug by @adamgibs in #345
    • SCRUM-1364 Experimental condition bug by @markquintontulloch in #347
    • ErrorMessage location is changed to under the editor for Editable tables by @kthorat-prog in #382
    • Table Header bleed through content fixed for other tables by @kthorat-prog in #379
    • Autocomplete search result for synonym fixed for Genetic Modifier field by @kthorat-prog in #408
    • SCRUM-1315 added code to address column reording issue by @adamgibs in #414
    • Bleed through in frozen edit column fixed by @kthorat-prog in #420
    • Fixed Frozen header and frozen column issue by @kthorat-prog in #422
    • Error message box alignment fixed by @kthorat-prog in #434
    • ZIndex made highest for errormessages component by @kthorat-prog in #435
    • Minor fixes by @markquintontulloch in #427
    • Quick fix for annotation returned object by @oblodgett in #415
    • SCRUM-1416 added null check to ListTableCell by @adamgibs in #388

v0.3.0

  • Data loading
    • Implemented NCBITaxonTerm class (SCRUM-338)
    • Enabled linkML format disease annotation submission (SCRUM-1203, SCRUM-122)
    • Loaded and added UI table for read and edit of Experminetal conditions data (SCRUM-1083, SCRUM-1082, SCRUM-725, SCRUM-1153, SCRUM-1154, SCRUM-1194)
    • Added better load reporting (counts and errors) (#289)
    • Fixed loading consistency and performance (SCRUM-1280, SCRUM-1281)
    • Added type suffix on data load download files (SCRUM-1067)
  • UI improvements
    • Added additional developer links in UI (#270, #271)
    • Enabled data customization session persistence (SCRUM-1036)
    • Enabled checkbox selection filter option for limited-option fields (SCRUM-1022)
  • Other
    • Added API authentication (SCRUM-1045)
    • Implemented flyway as DB schema managment solution (SCRUM-1054)
    • Serveral other fixes and improvements (#243, #245, SCRUM-853, #257, #263, #266, #274, #276, #293)

v0.2.0

  • Added UI login (authentication) (SCRUM-1034)
  • Enabled filter for Name in Genes Table (SCRUM-1058)
  • Added NCBI Taxonomy ontologies, including Id validation and autopopulation (SCRUM-338, SCRUM-1065)
  • Improved data load error handling display (SCRUM-972)
  • Enabled bulk submission of LinkML JSON files for disease annotations (SCRUM-984)
  • Fixed allele description sort & filter bug (SCRUM-1048)
  • Several UI fixes and improvements (SCRUM-852)

v0.1.0

  • Added and enabled update/edit on additional disease annotation properties
    • disease field (SCRUM-492, #110, #111, #112, #113, #114)
    • disease relation field (SCRUM-486, SCRUM-962, #119, #120, #132, #134, #135, #136, #137, #152, #153)
    • with field (SCRUM-706, #139, #142, #144, #145, #148)
    • evidence code (SCRUM-881, SCRUM-879)
    • negated field (SCRUM-498, SCRUM-498)
  • Changed curie to unique id for disease annotations #224
  • Loaded various ontologies:
    • MA (SCRUM-857, #141)
    • DAO (SCRUM-887)
    • EMAPA (SCRUM-892)
    • WBbt (SCRUM-873)
    • MP (SCRUM-948, #150)
    • ZFA (SCRUM-868)
    • XCO (SCRUM-102)
    • ZECO (SCRUM-102)
    • GO (SCRUM-897, #160)
    • CHEBI (SCRUM-902)
    • DO (SCRUM-277)
    • SO (SCRUM-1004, SCRUM-1006, SCRUM-1003)
    • Added obsolete colunm (SCRUM-1021)
  • Added Molecule class - loading and read-only diplay (SCRUM-335, #118, #122, #123, #124, #128, #143, #207, #213)
  • Added controlled vocabulary (SCRUM-570, #140)
  • Improved integration testing and automated run at PR validation (SCRUM-280, SCRUM-257, SCRUM-274)
  • UI improvements
    • Various search improvements (SCRUM-600, SCRUM-817, SCRUM-818, #131)
    • prevent updates adding obsolete DO terms (SCRUM-594)
    • Enabled sort and autosuggest on name/symbol fields for object/with columns (SCRUM-970, SCRUM-955)
    • Other autosuggest improvements (SCRUM-715)
    • Enabled user modification of UI data table display (SCRUM-1028)
    • various other fixes and improvements (SCRUM-851, SCRUM-971, SCRUM-499, SCRUM-969, SCRUM-710, #159, ...)
  • LinkML model updates (SCRUM-510)
  • Implemented automatic update loading of input files (#201)
  • Enabled central application logging (SCRUM-547)

v0.0.31

  • Setup additional application environments
    • Alpha environment (SCRUM-451, SCRUM-459, #83)
    • Beta environment (SCRUM-461, #102)
  • Cosmetic UI changes (SCRUM-568, #104, #100, #98, #97, #94)
  • Enabled in-table editing in disease annotation table
    • disease field (SCRUM-492, #90, #93, #101, #89)
    • subject field (SCRUM-473, #87, #86, #85, #84, #82, #75)
  • Added API endpoints to load disease annotations with evidence codes (SCRUM-322, #99)
  • Reduced reindexing failure rate (#95)
  • Integrated application compilation into Docker image building (#91)
  • Added integration testing for basic gene loading (SCRUM-248, #81, #80, #77, #74, #73, #72)
  • Added several testfile for later inclusion in integration testing (#71)
  • Temporarily disabled auto scaling (commit b54ebb8 in #76)
  • Other minor changes (#96, #92, #78, #69)