Release Notes ============= * 2026.4.3 * Support for read-only database mode for the GPF web layer, intended as a safeguard during production migration. * 2026.4.2 * Fixed eager loading for GPF instances. * 2026.4.1 * Extracted gain_core from dae — containing genomic_resources, annotation, task_graph, effect_annotation, utils * Renamed packages: dae → gpf, wdae → gpf_web * Renamed directories: gain → gain_core, gpf → gpf_core * Renamed satellite directories and packages to match new conventions: * gcp_storage → gpf_gcp_storage * impala_storage → gpf_impala_storage / gpf_impala2_storage * federation → gpf_federation * rest_client → gpf_rest_client * external_vep_annotator → gain_vep_annotator * external_demo_annotator → gain_demo_annotator * spliceai_annotator → gain_spliceai_annotator * Renamed legacy entry point groups (dae.*/wdae.*) * Added pytestarch architecture enforcement tests for the gain_core, gpf_core and gpf_web dependency direction * Added an about page and title to GRR repositories home page * Changed gene set descriptions * Fixed support for wildcard in score annotators * Fixed in-memory caching for CNV collection * Fixed fsspec protocol handling of about page markdown * Various ruff/mypy/pylint cleanups across all packages * Fixed build scripts, test runners, and package install names for the new structure * 2026.4.0 * Added caching for gene sets and gene scores. * Added warning for bigwig files with header mode. * Fixed 'internal' attribute handling in annotator configuration validation. * Fixes in GRR index page UI. * Refactored gene score validation and field naming. * Refactored gene score statistic building to use a single task. * Updated GRR resource page styling. * Added support for output file dependency tracking and intermediate output files in TaskGraph. * 2026.3.6 * Fix CNV collection annotator attributes' names. * Fix CNV collection annotator error handling when parsing filters. * Bug fix in GRR home page search functionality. * Fix gene score resource validation schema to support the type field. * 2026.3.5 * Added support for value type in gene score resources. * Fixes in GRR home page search performance and correctness. * Improved UI for GRR index page with support for copying resource IDs. * Added new serialization method to_dict for annotatable objects. This method provides a structured representation of the object's attributes and values. * Genomic resources summary descriptions cleaned up to remove markdown formatting for better readability in the UI. * 2026.3.4 * Fixed an issue with SQLite Full-Text Search index building. * String-type score fields now default to aggregate joining values with a comma separator instead of the previous default aggregator. * Fixed a bug in how VCF score definitions are merged. * 2026.3.3 * Added new annotator aliases for genomic score annotators. * Added Lark grammar support for cnv_filter in CNV collections. * Addedstring representation for annotatables. * Fixed default annotation handling for score annotators. * Updated GRR index page UI. * Full-text search support for resources in GRR. * Fixed filter parsing in CNV collections breaking on newline characters. * 2026.3.2 * Implemented backend resource search using APSW (SQLite via APSW library) * Added cached repository search support. * GRR index page selection now populated dynamically via script. * Fixed error status not being reset on empty query. * Added debounce to search input. * Added utility function to construct Annotatable objects from a plain dictionary * Annotation pipelines can now be loaded from .yml files in addition to .yaml * Renamed fetch_region_values method in the genomic score API. * 2026.3.1 * Support for full text search for resources in GRR home page based on SQLite FTS. * Fixes in handling of annotator attributes and annotator info serialization. * Fixed SpliceAI annotator plugin handling of annotator attributes and descriptions. * Support for empty default annotation in genomic resources. * Support for GPF_CONF_DIR environment variable for configuration of GPF instances. * Fixes in DuckDb genotype storage handling of memory limits and S3 support. * Bump version of DuckDb to 1.5.0. * Update support for filename patterns substitution in VCF variant loader. * 2026.3.0 * Fixed an error in attributes getter of score annotator. * Fixed VEP annototor build. * Fixed handling of work_dir in annotation pipeline and annotators factory. * Fixed handling of regions in schema2 SQL query builder. * Improved logging in liftover CLI tools. * Fixed fsspec repository protocols factory and serialization. * Bumped version of DuckDb to 1.4.4. * Bumped version of SQLite to 3.51. * 2026.2.5 * Refactor annotation pipeline factory to extract annotator building into its own function for better third-party access to annotator validation. * Exposed support for '--fork' flags in task executors CLI tools. * Improved debug logging in Dask executor for better visibility into task scheduling and execution. * Improved support for limiting the number of simultaneously running tasks in Dask executor to prevent resource exhaustion. * 2026.2.4 * Limit the number of simultaneously running tasks in Dask executor to prevent resource exhaustion. * Support for chaining tasks in TaskGraph. * Switch to using batches of task submissions in Dask executor for better performance. * Switch to collecting results in batches in Dask executor for better performance. * Improvements in synchronization and execution flow in Dask executor. * Reorganization of creation of statistics task creation for genomic resources. * Refactoring annotators to support explicit attribute and value types. * Added support for gene list attributes in effect and simple effect annotators. * Made empty annotation pipelines valid. * Refactoring annotation pipeline validation. * Fixes in Impala genotype storage. * Fixes in debug annotator. * Fixes in SpliceAI annotator plugin. * Bump version of Dask to 2026.1. * Bump version of fsspec to 2026.2. * 2026.2.3 * Fix of annotator info serialization. * Fixes in annotator configuration. * Fixes in serialization of GRR contents. * Support for compressed contents JSON file in GRR manage CLI tool. * 2026.2.2 * Added support for compressed contents JSON file in Genomic Resources Repository (GRR). * Fixes in build scripts. * 2026.2.1 * Performance improvements and fixes in gene profiles generation. * Switched to using task graph executor for parallel processing of gene profiles generation. * Added support for kwargs in task graph executor. * Switch to using stable variant counting mechanism in gene profiles generation. * Fixed handling of genomic scores in gene profiles generation. * Refactoring of annotators to use new mechanism for attribute descriptions. * Added new method `get_all_attribute_descriptions` to base class. * Added kwargs support for better task parameterization in task graph executor. * 2026.2.0 * Added support for spaces and single quotes in wildcard expression for annotation pipeline configuration. * Added support for validation of annotation pipeline configuration with wildcard expressions. * Added validation for empty annotation pipelines to raise errors instead of silent failures. * Switched to using Dask client map for task submission in TaskGraph executors for better performance and cleaner code. * 2026.1.4 * Refactoring of task graph executor infrastructure. * New TaskGraphExecutorBase class as unified base for all executors. * Added support for dynamic task ordering. * Major reorganization of task graph interface. * Improvements in gene profile generation performance. * Batched insertions for gene profile generation. * Removed redundant update calls with batched operations. * Further performance improvements in gene scores. * Improvements in annotator configuration and error handling. * Improved syntax for wildcard resource specification in annotation pipelines. * Error handling for wildcard matches in annotation pipelines. * Fixed NaN values returned by get_gene_value in gene scores. * Added process pool task graph executor for parallel processing of tasks. * Resource Statistics & Pickling (resource-statistics-tasks) * Improvements and fixes in pickling of fsspec repository protocols * Support for nonstandard UTR feature names in GPF gene models parser. * Support for missing gene_name in GTF gene models parser. * Improvements in demo_graph_cli tool. * 2026.1.3 * Added experimental thread pool executor for task graph execution * Experiments with process pool executor for parallel processing * Adjusted Dask executor for improved performance * Switched to using function scope for Dask client tests * Support for glob-like search in resource-repair tool * Fixed handling of broken resource state files * Support for score histograms without region splitting * Clean up task graph for genomic scores statistics * Fixed get_genes method to properly access column names (with test case) * Renamed gene score dataframe columns on creation * Fixed gene_list attribute in SimpleEffectAnnotator * Adjusted logging in query runners * 2026.1.2 * Fixed liftover chain caching and open operations. * 2026.1.1 * Changed gene scores to use column name similar to genomic scores. * Improvements in generate gene profiles CLI tool logging * Fixed handling of enrichment background models cache. * Fixed de Novo gene set collections building for datasets. * 2026.1.0 * Added support for finding resources by resource ID with version. * Support for specifying enrichment background models using resource_id and version. * Fixed enrichment coding length background tool. * Stable serialization of denovo gene sets. * Prevented WDAE study loading failures from breaking entire instance. * Added noreload option to wgpf. * Fixed study column configuration issues by making wrappers use config copies to avoid mutation. * Changed child searching in make_wdae_wrapper to use get instead of make. * Major refactor of DaskExecutor task scheduling using networkx topological sort. * Removed task2result dict from task executors. * Multiple cleanups and refactorings (_await_tasks, _process_completed). * Enhanced logging for debugging scheduling issues. * Improved executor efficiency through topological sorting. * In-memory caching for liftover chains. * Better handling of genomic scores fetching without region. * Support for edge cases in GRR manage CLI tool (region size less than or equal to 0). * Moved GPF documentation to separate gpf_documentation repo. * Updated to latest Sphinx version. * Removed obsolete dev dependencies. * 2025.12.0 * Fixed handling of allele scores on region boundary. * Improved test coverage for allele scores. * Fixed utility function for finding contig length in tabix or VCF files. * Improved test coverage for regions moudule. * Improved test coverage for QueryRunner and QueryResult base classes. * 2025.11.2 * Complete refactoring of all liftover CLI tools (VCF, DAE, denovo, CNV) * Fixed handling of region parameters and output filenames in liftover tools. * Comprehensive test suite added for liftover tools with extensive coverage including error handling. * Refactoring and doucmenting chromosome mapping annotator. * Added support for chromosome mapping in GeneModels resources. * Remove GeneModels.relable_chromosomes method. * Fixed annotation pipelien close method. * Fixed error messages for annotation pipeline creation errors. * Bumped DuckDb to version 1.4.2. * Bumped sqlglot to version 28. * 2025.11.1 * Reorganization of GeneModels for better maintainability. * Improved test coverage for GeneModels. * Improved GeneModels documentation. * Fixed allele score resource schema to support column_name and column_index. * Improved handling of study wrapper configuration. * Support for public URL in GRR definition. * Support for using annotate_columns and annotate_vcf as Python API. * Fixes in handling compression in annotate_columns and annotate_vcf tools. * Increased DuckDb memory limit for merging parquet files. * Fix handling of missing chromosomes in partition descriptor. * 2025.11.0 * Added chromosome mapping annotator to support removing and adding chromosome's prefixes during annotation. * Bumped version of DuckDb to 1.4.1. * Handling of missing chromosomes in variant loaders. * Improved error reporting in annotate_columns and annotate_vcf tools. * Dependencies management in Dask executor stopped relying on Dask API. * Support for compressed input in annotate_columns and annotate_vcf tools. * Adjustments in serialization of family variants. * Support for chromosome mapping in variant loaders. * Support for chromosome mapping in import genotypes tool. * Improved support for S3 genomic resources and genotype storages. * Switched to using MinIO for testing of S3 genomic resources and genotype storages. * 2025.10.7 * Bumped version to enable Google Analytics in production. * 2025.10.6 * Clean up typing and linting errors. * 2025.10.5 * Added support for merging score definitions in VCF based allele scores. * Expanded test coverage for genomic scores and genomic scores implementation classes. * 2025.10.4 * Improved description of annotator attributes to describe default and internal attributes. * Expanded SimpleEffectAnnotator to support gene lists and to report worst effect genes, gene effects and effect details. * Expanded EffectAnnotator support for gene lists. * Added support for gene list aggregators in EffectAnnotator and SimpleEffectAnnotator * The annotate_columns tool removes the intermidiary text file after tabix compression. * Fixes in handling of wildcard resources in annotation pipeline. * In-memory caching of loaded gene models. * Tuning configuration of Dask scheduler in named cluster. * annoate_columns and annotate_vcf tools support for reporting GPF version. * Expanded tests for gene models. * 2025.10.3 * Switched to using interval trees in GeneModels.gene_models_by_location method for better performance. * GeneModles factory functions are accessible from the gene_models package. * Effect annotation for regions and CNVs is ajdusted. * Fixed handling of variants that cross region boundary in annotate_columns and annotate_vcf tools. * Fixed and cleaned up SimpleEffectAnnotator. * Allowed parsing of CNV variants files without reference genome in annotate_columns tools. * Fixed support for CSHL variant format in annotate_columns tool. * Fixes and improvements in genomic context providers. * Support for disabling parallelization in annotate_columns and annotate_vcf tools. * 2025.10.2 * Reorganization and fixes in genomic context for annotation CLI tools. * Setting Dask scheduler default values for more adequate processing of annotation tasks. * Improved demo_graphs_cli tool for better testing of TaskGraph executors. * Fixed handling of variant queries in phenotype tool. * Fixed variant queries defaults in genotype studies and genotype storages. * 2025.10.1 * Fix gene set collection files property. * Fix GPF federation unit test. * 2025.10.0 * Fix gene set collection resourcse statistics hash. * Fix gene set annotator documentation. * Improved unit testing of gene set collection resources. * Continued improvements in GPF federation capabilities. * Improved handling of batches in SpliceAI annotator plugin. * 2025.9.7 * Revisited gene set collection resource implementation. * Split creation and loading of gene set collections. * New gene sets collection statistics computation for better handling of GRR management workflows. * Improved unit testing of gene sets collection resources. * Fixed handling of gene scores in GPF federation. * Fixed support for gene set in GPF federation. * Fixed handling of gene sets descriptions in GPF federation. * Improved handling of pagination in user management REST API. * 2025.9.6 * Fixes in Impala Schema1 genotype storage handling of affected status queries. * Fixed handling of zygosity in roles and sexes queries. * Fixed de Novo gene sets handling in GPF federation. * Updated SpliceAI annotator plugin documentation. * 2025.9.5 * Fixed support for de Novo gene sets in GPF federation. * Improved error reporting in VCF variants loader. * 2025.9.4 * Reorganization of intermediate files concatenation in annotate_columns tool. * Split tabix compres and tabix index into separate tasks in annotate_columns and annotate_vcf tools. * Keep existing columns in annotate_columns tool when appending new columns. * Fix region boundary handling in annotate_columns and annotate_vcf tools. * Added support for page_size parameter in GPF user and access managements APIs. * Fixed handling of zygosity in present in child and present in parent filters in genotype browser. * 2025.9.3 * Annotation tools improvements in handling working directories. * Support for '--keep-parts/--no-keep-parts' in annotation tools for for control over intermediate files. * Fixes in handling of logging verbosity in TaskGraph executors. * Fixes in handling of remote denovo gene sets in GPF federation. * Fixes in handling of remote studdies description in GPF federation. * Optimized remote studies handling of families by removing unnecessary families data. * 2025.9.2 * Fixed handling of batch size in annotate_vcf tool. * Improved VCF info field handling in annotate_vcf tool. * Reorganization of SpliceAI models loading in SpliceAI annotator plugin. * Improved packaging of GPF SpliceAI annotator plugin. * Improved memory management for import genotypes tool. * Fix handling of mypy py.typed in GPF wdae package. * Improvements in GPF federation query processing. * 2025.9.1 * Reorganization of cached GRR resource locking. * Improved resource management in variant loaders. * Improvements in task forking in TaskGraph. * Fixes in handling of remove alleles in federation variants processing. * Fixes in genotype storage plugins. * 2025.9.0 * Major Django framework upgrade from 4.2.17 to 5.2.5 * Reorganization of Genotype Storage registry and queries. * Improved support for phenotype browser support in GPF federation. * Improved support for common reports in GPF federation. * Improved GPF federation and REST client testing. * Fixed support for summary variants queries and support for filtering by summary variant IDs. * Fixed resource management in processing annotation pipelines. * Added support for task forking in TaskGraph. * Extensive mypy and lint error cleanup across the codebase. * Improvements in GPF SpliceAI annotator plugin resource management and cleanup. * Reorganization of phenotype registry studies loading. * Support for parquet datasets in import projects input section. * Fixed support for remote gene sets in enrichment tools. * Fixed support for remote families download. * Fixed support for remote measures variants queries. * 2025.8.1 * Improved batch support for INDELs in SpliceAI annotator plugin. * GPF SpliceAI annotator plugin added to GPF releases. * 2025.8.0 * Reorganization of annotation tools and annotation infrastructure. * Reorganization and improvements in GPF federation plugin testing. * Improvements in federation Enrichment tool. * Enhanced remote study wrapper with comprehensive unit testing. * Added gene view support in GPF federation. * Fixed remote configuration handling. * Reorganization and improvements of GPF REST client library. * Bumped DuckDb to version 1.3.2. * Use DuckdDb for parquet files merging in Schema2 import tool. * Fixed DuckDb S3 AWS support with proper secret clause handling. * Reduced memory usage of ParquetLoader. * Added support for manual cluster in Dask client configuration. * Support for batch mode in SpliceAI annotator plugin. * Bump version of Angular to v19. * Improvments in phenotype tools user interface state handling. * 2025.7.1 * Fixes in federation enrichment tool. * Extended unit testing of GPF federation plugin. * Improvements in gpfjs handling of histogram validation. * 2025.7.0 * Reorganization of parquet processing and merging for better maintainability and reduced memory footprint. * Reorganization of enrichment tool for better support of federation of GPF system. * Improved support for remote genotype and phenotype studies in GPF federation. * Bumped version of Python to 3.12. * Fixes in TaskGraph logging and progress management. * Fixes in query variants download view. * Fixed closing of DuckDb connections in phenotype browser. * Improved query heuristics in SQL query builder. * Extensive mypy and lint error cleanup across the codebase. * Improvements in gpfjs handling of histogram validation. * 2025.6.4 * Reorganization of variants processing in Schema2 import genotypes. * 2025.6.3 * Reorganization of phenotype tool adapter class. * Bump PyArrow to version 20.0.0. * Reorganization of storing study configs in import storages. * Reorganization of variants parquet writer classes. * Improved unit testing of histogram component in GPFjs. * 2025.6.2 * Fix error state reset for gene sets and gene scores user interface components. * Start using genomic context in Schema2 import gentotypes tool. * Fix handling of study description in GPF federation. * Bump DuckDb version to 1.3.1. * Support for fetch variants in variant loaders. * Fix support for phenotype studies in GPF federation. * 2025.6.1 * Improved unit testing of gene models. * Improved handling of Lark variant queries. * Reorganization of genomic contexts workflow. * Fix ped2ped initialization using genomic context. * Move GPF user documentation from gpf_documentation to the GPF repository. * Reorganization of phenotype tool in GPF federation. * Support for serialization of variant blobs into Avro format. * Fix handling of phenotype measure filters in phenotype groups. * Support for phenotype studies in GPF federation. * Reorganization of initial state loading for user interface components of genotype browser. * 2025.6.0 * Bump DuckDb to 1.3.0 * Improve error handling in genotype browser variants rows creation. * Improve tooltip color scheme. * 2025.5.10 * Clean up federation plugin testing. * Fix and improve support for gene sets in federation plugin. * Clean up wdaemanage tool. * Update link description about registration on the login page. * Clean up family and person filters user interface. * Round decimals in value domain in phenotype browser. * Add info icon for enrihment tool background models. * 2025.5.9 * Hide phenotype browser NaN values. * Stop hover on phenotype browser measure column. * Reorder logging configuration inf wgpf tools. * Fix handling of visible datasets in federation plugin. * 2025.5.8 * Fixes in handling of table preview in genotype browser. * Limit y-axis ticks in histograms. * Refactor federation loading of remote studies. * Pin the version of importlib-metadata to workaround Dask issue. * Fix warning for wrong gene_scoores column configuration. * Fix setting zygosity filters in genotype browser UI. * Clean up creation of federation tokens user interface. * 2025.5.7 * Fixing support for denovo gene sets in federation plugin. * Clean up federation plugin testing infrastructure. * Support for update of phenotype measures and instrument descriptoins. * Fix proagation of any_user permissions to dataset parents. * Fix in liftover annotator. * Fix federation support for person set collections. * Fix federation support for studies hierarchy. * Keep additional attributes in denovo_liftover tool. * 2025.5.6 * Remove debounce time in phenotype measure role searching. * Support markdown in phenotype browser measure and instrument desciption. * 2025.5.5 * Reorganization of GPF federation plugin. * Fix support for CNV in variants query grammar. * Fix regions filter text area. * 2025.5.5 * Reorganization of GPF federation plugin. * Fix support for CNV in variants query grammar. * Fix regions filter text area. * 2025.5.4 * GPF federation regorganization. * Support for phenotype instruments and measures update. * Fix VEP annotator plugin for newer version of VEP. * Bump version of Lark parser library to 1.2.2. * Update GRR gene set collection info pages. * Clean up dae and wdae testing infrastructure. * Clean up phenotype browser measure domains. * Support for instruments and measures tooltips in phenotype browser. * 2025.5.3 * Fix handling of phenotype measures error state in GPFjs. * Update GPF federation plugin. * Reorganization of GPF instance adjustements tool. * 2025.5.2 * Fix rebuilding of phenotype browser cache in wgpf tool. * Clean up common reports logging. * Adjust default working directory for genotype import tool. * Allow editing of home page description when permissions are disabled. * Fix Y-axys ticks in histograms. * Fix validation of gene symbols in genes component. * Support for automatic table preview in genotype browser. * 2025.5.1 * Fix support for queries by role. * Allow missing work directory in phenotype data import project. * Support for instrument description in phenotype data import project. * Remove study phenotype from default study configuration. * Fixes in gene symbols validation. * Fixes in histograms y-axis labels. * 2025.5.0 * Fix support for default configuration of denovo gene sets. * Clean up CLI tool for generation of denovo gene sets. * Invoke the CLI tool for generation of denovo gene sets from the wgpf tool. * Fixes in GPF federation plugin. * Fixes in gene symbols validation. * 2025.4.10 * Fix grr_cache_repo tool to use embedded annotation configuration. * Improve performance of re-annotation tool checks for reannotation. * 2025.4.9 * Fix CNV variants frequency filtering. * Support for default commont report configuration for phenotype data. * Support for default study configuration with download columns from annotation. * Fix default configuration of phenotype measure filters. * Clean up phenotype browser cache build tool invocation in wgpf tool. * Fix default configuration of enrichment tool. * Add link to registration info into login page. * Fix keybindings in phenotype measrues filters. * Fix phenotype measures description popup dialog. * 2025.4.8 * Fix default CNV study configuration generated at import in DuckDb genotype storage. * Auto-scroll to table preview in the genotype browser when results are loaded. * Fix tool selection bug when navigating from Gene Profiles to Gene Browser. * Enhance separation of internal and external links in Gene Profiles single view. * Reset zygosity filters when switching between datasets. * 2025.4.7 * Fix phenotype browser cache regeneration in wgpf tools. * 2025.4.6 * Fix heuristics for Y log scale in histograms. * Fix roles queries in legacy genotype storages. * Support for filters by zygosity in sexes in DuckDb genotype storage. * Change default columns in DenovoLoader format. * Add timeout argument to the GPF REST client query variants method. * Fix de Novo icon in dataset dropdown and hierarchy. * Fix loading pheno measure filters from UI state. * 2025.4.5 * Enable pheno measure filters by default when a genotype study has phenotype data. * Genotype data groups should deduce has_denovo and has_transmitted flags from children. * Enable pheno tool by default when a genotype study has phenotype data and de novo variants. * Support for filters by zygosity in roles in DuckDb genotype storage. * Adjust default study configuration to make GSG fluent. * Fix pheno measure filters user interface. * Reorganize genotype browser filters ordering. * Support for filters by zygosity in Present in Child and Present in Parent in genotype browser. * Fix histograms bars with zero height. * Support pheno measure description in pheno measure filters. * 2025.4.4 * Support for queries by zygosity in roles in DuckDb genotype storage. * Support for inlining annotation in GPF instance configuration. * Adjust import genotypes CLI tool default working directory. * Adjust import phenotypes CLI tool default working directory. * Support for automatic re-annotation in wgpf CLI tool. * Fix pedigree loading in phenotype studies. * Fix phenotype studies pedigree downloads. * Update default genotype data configuration. * 2025.4.3 * Bug fix in handling of permissions on phenotype data. * 2025.4.2 * Fix command line tool for generation of dataset statistics. * Fix phenotype data families data to load family tags. * Fix queryies by family tags in Apache Impala Schema1 genotype storage. * Support for queries by zygosity in statuses in DuckdDb genotype storage. * Fix in liftover annotator. * 2025.4.1 * Consistent CLI interface and implementation for all annotation. * Support for common reports in phenotype data groups. * Reorganization of datasets hierarchy user interface. * Switch to using DuckDb genotype storage for default internal storage. * Reorganization of GPF rest client tokens. * Genotype storage support for query by family tags. * Fix support for INDELs in SpliceAI annotator plugin. * Support for more attributes and aggregation of attributes in SpliceAI annotator plugin. * 2025.4.0 * Fix values domain ordering in phenotype data import. * Fix GRR histogram labels on X-axis in case of X log scale. * Initial implementation of SpliceAI annotator plugion. * Support for validation in gene symbols edit box in genotype browser. * Fix visual bug in Safari browser in gene profiles single view. * 2025.3.7 * Fix present in parent default values in phenotype tool. * Bump dependencies versions. * Clean up testing of GRR HTTP protocol support. * 2025.3.6 * Fix present in parent default values. * Support for getting roles from phenotype data groups. * Fix VEP annotator plugin attributes types. * 2025.3.5 * Fix gene profiles search for gene symbols. * Clean up VEP annotator plugin documentation support. * Fix VEP annotator plugin open method. * Support for configutation of histograms in phenotype data import. * Support heuristics for log scale Y axis in histograms. * Fix sorting of gene consequences in VEP annotator plugin. * Fix handling of genome prefix in regions filter block. * 2025.3.4 * Clean up handling of genome prefix. * 2025.3.3 * Fixes in VEP annotator plugin. * Updates in CNV collection annotator. * Fixes in handling of .gz files in annotate columns tool. * 2025.3.2 * Extend support for genomic context in all annotation tools. * Fixes in GPF REST client library. * Support for phenotype measures filtering by role. * Support for batch annotation in import tools. * Fix GTF parsing and serialization. * Clean up enrichment tool configuration. * Fix handling of categorical histograms labels. * Fix transmitted rare variants filter. * Improvements in categorical histograms user interface. * Update phenotype family and person filters to include roles. * 2025.3.1 * Fix permissions for any_user group with annonymous user. * Fix in handling of empty lines in VEP annotator plugin. * Fix GRR histograms modals. * Fix VEP annotator plugin handling of unknown attributes. * Clean up GRR manage tool support for single region tasks. * Add VEP annotator plugion tool for cache download. * Fix VEP annotator plugin writing to context. * Fix handling of whitespaces in dataset description. * Improvement in handling of labels in categorical histograms. * Fix categorical histograms handling of order in categorical histograms. * 2025.3.0 * Fix datasets hierarchy with hidden datasets. * Fix ordering of studies in genotype data groups. * Support for label rotation in categorical histograms. * Expand gene set collection GRR info page. * Fix support for phenotype person and family filters in genotype browser. * 2025.2.2 * Fix phenotype group hierarchy construction. * Fix access rights for datasets hierarchy requests. * Fix genomic scores header width. * Update person filter styles. * 2025.2.1 * Support VEP annotator plugin using VEP Docker container. * Support for phenotype mearures filtering using value and histogram types. * Support for description in phenotype studies. * 2025.2.0 * Update gene profiles configuration. * Introduction of phenotype storage and phenotype storage registry * Support phenotype data into datasets hierarchy * Update and fix CNV collection statistics * Improvements in phenotype data import and phenotype browser cache * Initial support for VCF serialization of full variants iterator from variant loaders * Support for phenotype data common reports * Support for full pedigree information in phenotype data import * Adjust wgpf tool to support phenotype data stides and groups * Support for categorical histograms label rotation * Fix for phenotype data group merge instruments function * Support for categorical genomic scores in the UI * Support for multiple views for categorical histograms UI * Support for label rotation in categorical histograms UI * 2025.1.4 * Fix deserialization of variant attributes. * 2025.1.3 * Clean up phenotype browser cache build tool. * Fix support for categorical genomic scores queries. * Deprecation of `import_tools` and introduction of `genotypes_import`. * Deprecation of `import_tools_pheno` and introduction of `phenotypes_import`. * Fix support for categorical histograms for genomic scores. * 2025.1.2 * Fix wgpf tool. * 2025.1.1 * Fix queries by present in child and present in parent. * 2025.1.0 * Update the model for saving queries. * Gene Browser performance optimization. * Added support for downloading Phenotype Tool report image. * Fix OAuth2 login request to use the proper encoding. * Fix OAuth2 authentication. * Bump version of Angular to v18. * Fix gene profiles single view back navigation for gene not found. * Support for categorical histograms in genomic scores user interface. * Improved unit tests coverage for GPFjs. * Bump versions of ECMAScript and TypeScript. * Extention of GPF REST client to support more REST API endpoints. * Switch to using DuckDb for gene profiles. * Fix handling of internal annotation attributes in annotate_vcf. * NormalizeAlleleAnnotator to support discovery of the reference genome if not specified in the annotation pipeline. * Change the VEP annotator plugin to use VEP in offline mode. * Reorganization of genomic scores resources hierarchy. * Reorganization of genomic scores annotators hierarchy. * Fix gene regions heuristics. * Performance improvements in VCF variant loader. * Support for no region split in grr_manage. * Implementation of GPF instance re-annotation tool. * Reorganization of handling of pedigrees. * Added index file in GRR statistics folders. * Fixes in family roles builder class. * Switch to using Pyright in GPF builds. * Split of the phenotype data import into separate tools. * Support for phenotype data import project. * Performance improvements in import of VCF studies in Schema2. * Fix calcuation of variant types in VCFAllele annotatable. * Clean up of GPF unit tests. * Reduction of memory footprint in Schema2 parquet writer. * Reduction of memory footprint for import tools. * Fix default `fill-in-mode` for VCF variant loader. * Refactor phenotype import measure classification. * Refactor tools for building phenotype browser cache. * Refactor phenotype data registry. * Bump GPF dependencies versions. * Switch CNV collection to use genomic scores base class. * Fix query variants for studies without variants. * Support queries by affected status in Schema2 genotype storages. * Support for queries by categorical genomic scores. * 2024.12.2 * Fix the GTF gene models parser. * Change the fetch_region method signature for genomic scores. * Fix for usage of .CONTENTS file in GRR. * 2024.12.1 * Fix support for GRR contents file in YAML format * 2024.12.0 * Restore gene scores partitions REST API * Clean up WDAE unit tests * The cnv_collection does not crash on an unknown chromosome * Added get_region_scores to PostionScore interface * Change `fetch_region` method signature for `AlleleScore` * Switch to using JSON format for GRR contents file * Reorganization of GeneSetAnnotator to support multiple gene sets * Fis support for downloading phenotype tool report image * Restore usage of gene scores partitions * 2024.11.3 * Fix annoate_columns to create a correct tabix index * Fix SimpleEffectAnnotator to produce a link to the GPF documentation * Adjust formatting of float numbers in annotate_columns and annotate_vcf tools * Fix gene set annotator to include attributes in the annotation schema * Fix gene score annotator documentation to include aggregator * Add support for read-only filesystem GRR * Add support for liftover annotator to use source and target genomes from liftover chain genomic resource labels * Annonymous users can access limited functionality of phenotype tools * Add support for effect annotator to use reference genome from genomic resource labels, annotation pipeline preamble, and genomic context * Fix types produced in annotation pipeline documentation * Fix dataset hierarchy permissions * Support for wildcards in annotation pipeline resource_id annotator's attributes * Fix in region splitting in annotation and reannotation tools - annotate_columns, annotate_vcf and annotate_schema2_parquet * Support for categorical histograms in gene scores user interface * Support for consistency checks in genomic scores fetch_region method * Minor optimizations in the genomic position table * Fix an infinite loop in the liftover annotator * Minor improvements in DuckDb genotype storage * Support for downloading phenotype tool report image * Fix in the error handling for family filters in the genotype browser * 2024.11.2 * Fix pheno import type inference issues * Improvments in phenotype data import unit testing * Improvements in enrichment REST API unit testing * Fix handling of `any_user` access rights in dataset hierarchy * Fix query cancelation in gene browser * 2024.11.1 * Fix pheno import type inference issues * Improvments in phenotype data import testing * Construct gene sets download ling on the frontend * Fix handling of frequency filters in DuckDb genotype storage * Bump version DuckDb to 1.1.3 * Implementation of full re-annotation of schema2 parquet datasets * Factory functions for bulding genomic resources from resource ID * Fix query cancelation in genotype browser * Improvement in handling pedigrees in dataset statistics without access rights * 2024.11.0 * Pure python implementation of type inference for phenotype measures * Phenotype data import refactored * Support for storing gene models in GTF format * Support for storing gene and genomic scores histograms in JSON format * Fix de Novo gene sets user interface * Fix hanling of families and persons IDs in save/share query * 2024.10.6 * Bug fix in handling genomic scores with chromosome remapping * Workaround for pysam handling of HLA contigs regions * Bug fix for handling dataset description without children * 2024.10.5 * GPF federation refactoring to create a separate conda package *gpf_federation* * Update de Novo gene sets REST API * Support for restricted access of GPF tools without explicit access rights * Improvement and fixes in Schema2 parquet datasets re-annotation * Bump DuckDb version to 1.1.2 * Support for DuckDb S3 genotype storage * Fix missing gene profiles state in GPFjs * 2024.10.4 * Refactor and fixes in support of person set collection queries * 2024.10.3 * Remove an exception logger from phenotype measures download in phenotype browser * 2024.10.2 * Clean up user edit code from GPFjs * 2024.10.1 * Bump Angular version to 17 * Bump DuckDb version to 1.1.1 * Fix Impala genotype storage bugs * Clean up dataset statistics unit tests * 2024.10.0 * Bump Angular version to 16 * Clean up of GPFjs code * Fix annotatoion pipeline documentation links to genomic resources * Support for full VEP annotation in VEP annotator plugin * Reorganization of de Novo gene sets API * 2024.9.3 * Fix phenotype measures download in phenotype browser * Fix searches for datasets in management user interface * Fix datasets permissions REST API * 2024.9.2 * Support search for datasets in management user interface * Fix denovo report generation * Remove duplicated large and small value labes in genomic scores histograms help modals * Fix bigWig genomic position table fetch method * Fix inmemory genomic position table handling of zero based scores * Fix handling of displayed_values_percent in categorical histograms * 2024.9.1 * Fix default number of bins in genomic scores histograms * Support case insensitive search in phenotype browser * Update links to annotators documentation in annotation pipeline documentation * Add missing files method in gene sets genomic resource implementation * Fix handling of ultra rare heuristics in DuckDb genotype storage queries * Clean up and imporements in wdae unit testing * Fix hanlding of zero based scores in inmemory genomic position table * Fix phenotype browser table sorting buttons state * Refactor and clean up of GPFjs internal state handling and transition to ngrx * 2024.9.0 * Performance improvements in annotation with bigWig scores resources * Bug fixing in wdae datasets API hierarchy * Phenotype data import type inference improvements * GPF validation runner error reporting improvements * BigWig genomic resources buffering Improvments * Phenotype data import of browser data improvements * Phenotype browser table improvements * Support for integer region bins in schema2 genotype storages * Schema2 Parquet loader fixes in hadling of regions * DuckDb genotype storage reorganization * Support for DuckDb genotype storage over S3 * Separate GPF federation into a package ``gpf_federation`` * Revisit histogram configuration and support for user defined plot functions * Improvements in ``gpf_wdae`` unit testing * 2024.8.2 * Improvement of SQL query builder for family and summary variants in DuckDb genotype storage * Fix packaging of external VEP annotator plugin * Support for serialisation of additional attributes of family variants * Fix support for log-scale Y axis in categorical histograms * Fix loading of gene profiles search term from gene profiles state * 2024.8.1 * Fix caching of genotype data groups descriptions * Genomic position table optimization for bigWig resources * 2024.8.0 * Fix for pheno data import on clusters * Fix genomic scores histograms large and small value labels * Change genomic scores configuration to support `column_name` and `column_index` * Fix support for genomic scores with `zero_based` genomic position table * 2024.7.8 * Fix handling of bigWig resources with chromosome mapping in `grr_manage` * 2024.7.7 * Added unit tests for external VEP annotator plugin * Fix collection of study parents in `gpf_wdae` * Fix bigWig genomic position table fetch method * Fix annotation pipeline preamble * Fix gene browser input field behavior in GPFjs * Fix query cancelation on destroy of component in GPFjs * 2024.7.6 * Added web caching for GPF instance home and about pages * Fix handling of permissions for `any_user`` group in `gpf_wdae` * Fix gene profiles single gene search from home page * Clean up old dataset description cache in GPFjs * Fix search query cancelation in phenotype browser * Fix handling of description for annonymous users in GPFjs * Fix in dataset selector dropdown in GPFjs * 2024.7.5 * Performance improvements in calculation of access rights for datasets * Fixes in datasets routing in GPFjs * Added UI for resetting gene profiles state * 2024.7.4 * Fixes in pheno measures dropdown selector for genotype browser and pheno tool * 2024.7.3 * Bump versions of django dependencies * Fix handling of phenotype data groups * Fix sorting of pheno browser table * Gene profiles user interface state store in user profile * Improvement in enrichment tool results display * Fixes in `gpf_validation_runner` tool * Fixes for serialization of gene models in GTF format * Fix chromosome mapping for bigWig genomic position table * Fix in phenotype tool user interface controls * Fix in gene browser user interface coding only control * Fix in histogram sliders user interface * Fixes for handling of selected dataset in GPFjs internal state * New pheno measures dropdown selector for genotype browser and pheno tool * 2024.7.2 * Tool for drawing score resources histograms `draw_score_histograms` * Gene sets clean up and fixes * Fix handling of internal buffer of tabix genomic position table * 2024.7.1 * Improvements in genomic position table performance * Initial support for 0-based genomic scores in genomic position table * Initial support for serialization of gene models in GTF format * Fix in handling of saved queries in GPFjs * 2024.7.0 * Bump Python version to 3.11 * Fix in gene profiles search for genes * Support for browser caching of GPF wdae requests * Support for style tag in GRR info pages resource description * Support for ZSTD compression of variants data blobs in schema2 parquet * Fixes in annotation pipeline construction * Fixes in support for bigWig format in genomic scores * Fixes in handling of selected dataset in GPFjs * Fixes of visual flickering of dataset selector dropdown in GPFjs * Fixes in handling of internal state in GPFjs * 2024.6.6 * Update for GRR info pages for genomic scores, gene scores, gene models and reference genome * Demo annotators for external tools using batch mode annotation * Demo annotators for external tools using using GRR resources and batch mode annotation * Fixes and optimization for genotype variants query over schema2 parquet loader * Fix handling of bigWig resources in GRR * Fix home page search for a gene profile * Fix handling of gene browser input * 2024.6.5 * Fix for GTF gene models parser * 2024.6.4 * Initial support for batch mode in annotation pipeline and annotate columns tool * Fix for gene profiles state handling in GPFjs * Clean up and improvements in searchable dropdowns in GPFjs * 2024.6.3 * Fix gene scores missing description in GRR info pages * DuckDb version bumpted to 1.0.0 * Initial implementation of request caching in WDAE * Fix a minor issue in collapsable dropdown dataset selector * 2024.6.2 * Initial support for BigWig genomic resources * Bump GPF dependencies * Fix handling of phenotype browser images * Improved gene models statistics * Improved gene models and reference genome info pages in GRR * 2024.6.1 * Fix gene models GTF parser * Parallelization of phenotype data import tool * 2024.6.0 * Fix in hadling annotation pipeline preamble in annotation documentation tool * Imrovements in annotation documentation tool * Support for quering genotye variants over Schema2 parquet loader * Improvements in genomic scores and gene scores info packages * Fix in handling studies without variants in GCP Schema2 genotype storage * Fix in family tags counter * Collapsable dropdown dataset selector * Fix phenotype tool legend * Fix the layout of histogram description in scores descriptions * 2024.5.3 * Fix hanlding of genomic resources varsions in GRR home page * Support for multiple regression measures in phenotype databases * Resore basic liftover annotator * Fix in handling studies without variants in Impala Schema2 genotype storage * Improvments in handling annotation pipeline preamble section * Fix alignment of dataset names in GPF home page hierarchy * Fix handling of gene profiles column ordering * Fix families counter in dataset statistics families by pedigree page * 2024.5.2 * Improved styling of annotation documentation generated by annote_doc * Fix handling of `hidden` datasets in GPF home page hierarchy * Bug fix for loading datasets in GPFjs * 2024.5.1 * Annotation pipeline as genomic resource * Improvements in liftover annotator * Store column ordering in gene profiles state * Fix resizing of phenotype browser table * Source maps instrumentation of GPFjs build * 2024.5.0 * Support for preamble in annotation pipeline * Support for genotype studies without variants * Improvements in loading dataset hierarchy performance * Full parquet datasets variants loader * Store gene profiles visible columns to state * Fix handling of invalid URLs