htsget-search-v0.2.0

Added

• (test) add multiple resolvers for server tests and test resolution
• use serve_at in data server rather than a constant
• (config) add automatic config inference for local and s3 storage, and rearrange modules
• [breaking] simplify storage config by allowing untagged enum representation

Other

• (search) convert match to if let
• (search) add warning when a non-valid PL read group header is found
• (search) add additional tests for searching resolvers and from storage
• (search) implement ResolveResponse on HtsGetFromStorage
• [breaking] rename HttpTicketFormatter and remove UrlFormatter implementation for it
• [breaking] move htsget structs to config, and resolve storage type in config

htsget-lambda-v0.2.0

Added

• (test) add multiple resolvers for server tests and test resolution
• (config) add automatic config inference for local and s3 storage, and rearrange modules
• [breaking] simplify storage config by allowing untagged enum representation

Other

• [breaking] rename HttpTicketFormatter and remove UrlFormatter implementation for it
• [breaking] move htsget structs to config, and resolve storage type in config

htsget-http-v0.2.0

Added

• (config) add automatic config inference for local and s3 storage, and rearrange modules
• [breaking] simplify storage config by allowing untagged enum representation

Other

• [breaking] rename HttpTicketFormatter and remove UrlFormatter implementation for it
• [breaking] move htsget structs to config, and resolve storage type in config

htsget-config-v0.2.0

Added

• use serve_at in data server rather than a constant
• (config) set Local resolvers from data server config after parsing the Config
• (config) add automatic config inference for local and s3 storage, and rearrange modules
• [breaking] simplify storage config by allowing untagged enum representation

Other

• (config) fix typo
• (config) rename test
• (config) add tests for resolving responses
• (config) fix incorrectly using resolved id when searching for regex capture groups
• a few style changes, changed default resolver
• (config) add tests for default tagged storage type
• (config) document new features and how to use them
• [breaking] rename HttpTicketFormatter and remove UrlFormatter implementation for it
• [breaking] move htsget structs to config, and resolve storage type in config
• (config) leverage tagged enum types to allow selecting storage type without manually specifying config values

htsget-actix-v0.2.0

Added

• (test) add multiple resolvers for server tests and test resolution
• (config) add automatic config inference for local and s3 storage, and rearrange modules
• [breaking] simplify storage config by allowing untagged enum representation

Other

• a few style changes, changed default resolver
• [breaking] rename HttpTicketFormatter and remove UrlFormatter implementation for it
• [breaking] move htsget structs to config, and resolve storage type in config

htsget-test-v0.1.4

Other

• Set MSRV on all sub-crates (#146)

htsget-search-v0.1.4

Fixed

• fixes for byte range ends
• fix IOError name
• fixes & model improvements & bam search progress
• fixes & model improvements & bam search progress
• fix docs

Other

• Set MSRV on all sub-crates (#146)
• Better CI (#98)
• Merge branch 'main' of https://github.com/umccr/htsget-rs into more-flexible-config-rename
• add test for long resolvers from environment variable config
• clippy and fmt
• allow specifying tags, reference names, fields with an 'All' value
• reduce some options for cors, remove repeated code when configuring cors
• fix tests affected by config, change some default values and move around config options
• apply changes to other crates from reworked config
• deserialize empty string as None value
• move cors config to separate file
• fix errors relating to new config
• add tests for checking for contained value in interval
• add safe cast for conversion between i64 and u64
• move fields, tags, no tags, query, and interval to config
• Make search structs public
• Remove ReferenceSequenceInfo
• Remove unused code and logic
• Add tests for no end position
• Remove requirement for default end position when converting to noodles interval
• Merge branch 'main' of https://github.com/umccr/htsget-rs into exports
• Export some functions for use as a dependency
• Re-export htsget-config as a dependency from other crates
• Update non-noodles dependencies
• Http and tls server test uses test utils
• Convert preflight server test to test utils
• Convert data server test to use test utils
• Implement http test traits for data server
• Add CorsLayer responses to htsget-http-lambda
• Move configure_cors to module file
• Bump deps for noodles and simplify logic around maximum reference sequence length using new noodles types
• List out allowed methods rather than sending wildcard
• Add ticket server cors tests
• Add cors options request test
• Fix tests implementation
• Can't use base directory function in test
• Implement additional cors test
• Add base path only function in tests for code reuse
• Add cors tests
• Layer should go after merge
• Implement cors for data server
• Rename ticket server to data server
• Move data server config to separate struct
• Implement cors for htsget-http-actix.
• Changes to deployment (#116)
• Remove some trace log details to avoid making them overly long.
• Add more detail to gzi traces.
• Add more spans and tracing calls.
• Add buffered reading to bai and gzi.
• Add buffered reading to cram search.
• Remove logging chunks as it is too noisy.
• Emit trace logs from functions.
• Add some more instrument targets, use span in_scope.
• Remove sleep call.
• Add a few more tracing span targets.
• Add span tracing to test timings.
• Small changes related to indices (#114)
• Bump dependencies, fix clippy warnings.
• Avoid reading index unless it is required.
• Remove some unnecessary unwraps.
• Improve errors so that they are more informative.
• Remove RangeBounds on BytesPosition as its use is less readable with classes.
• Fix tests related to response class.
• Remove headers from response if empty.
• Simplify JsonUrl logic.
• Responses should contain a class for all ranges, or no ranges.
• Fix tests.
• Implement RangeBounds for BytesPosition.
• Perform byte position merging when creating data blocks.
• Byte position records class, Header for only header bytes, Body for only body bytes, and None if there is a mix of bytes.
• Allow BytesPosition to record its own class.
• Fix unneseccary storage queries (#107)
• Simplify querying for all records by determining file size.
• Server benchmarks should use non-tls ticket server as this is a fairer comparison to the htsget-refserver.
• Clean up code, format, update dependencies.
• Tests run independently by using dynamic port allocation.
• The GC info field should have a Float type rather than an Integer type.
• Implement non-tls ticket server alongside tls ticket server.
• Rename some traits and structs to clarify their purpose.
• Bump many deps (except querymap) and avoid pulling full tokio in, we just need macros and rt-multi-thread (#96)
• Out of order urls (#95)
• Pinning to noodles-tabix =0.9.0 as suggested in zaeleus/noodles#90 (comment) as a result of getting CI errors on https://github.com/umccr/htsget-rs/runs/6803593182?check_suite_focus=true#step:6:90
• Fix eof errors (#87)
• Add benchmarks (#59)
• Fix localstorage path (#86)
• Fix tests and errors (#83)
• Deploy htsget-http-lambda. (#81)
• Enable choosing between storage types. (#80)
• Remove file from localstorage (#79)
• Spawn s3-server once so that tests don't have to be run on one thread. (#78)
• Remove blocking (#77)
• Htsget http lambda (#76)
• Storage class for s3 (#74)
• Decouple File struct from Search trait. (#70)
• Fix runtime panics from curl (#69)
• Bump all tokio versions and stay on track with Noodles versioning instead of working from its git /cc @andrewpatto
• Implement id resolver (#60)
• Convert Storage and HtsGet traits to use async/await (#56)
• Bump up noodles across crates, otherwise several versions get mixed up
• Add the service info endpoints (#54)
• Add the htsget-http-core and htsget-http-actix crates (#45)
• Track crates.io version of noodles (#53)
• Use file size for end bytes ranges.
• Refactor commonalities across all formats.
• Providing the file size through the Storage abstraction. (#49)
• Implement CRAM search backend. (#44)
• Add BCF support (#43)
• Improve the bytes ranges for the BAM header (#42)
• VCF search interface implementation (/variants endpoint) (#37)
• Adapt tests to noodles changes (#41)
• Htsget tests (#40)
• Calculate BAM byte ranges more accurately (#35)
• Remove duplicity in Query, UrlOptions and Url (#29)
• Fix Local Storage always adding the Range header (#31)
• Storage model tests (#28)
• Merge pull request #25 from chris-zen/vcf_bcf_test_data
• Add some tests for LocalStorage::url (#22)
• Add the rest of the builder methods to Query (#21)
• Implement class attribute for reads. (#19)
• Update references and README (#18)
• add tests for BytesRange (#14)
• merge byte ranges
• some renames
• Fix BAM search for unmapped & clippy errors
• add search by reference name and range
• add TODO for BamSearch::url tests
• add TODO for BamSearch::url tests
• added test for HtsGetFromStorage
• added 2 tests for BamSearch
• preparing tests for BamSearch
• add tests and fixes for LocalStorage
• reorganized + rustdocs
• introduced the concept of Storage
• failed attempt to use a BAI index
• work in progress

htsget-lambda-v0.1.4

Other

• Set MSRV on all sub-crates (#146)
• Better CI (#98)

htsget-http-v0.1.4

Other

• Set MSRV on all sub-crates (#146)
• Better CI (#98)

htsget-config-v0.1.4

Other

• Set MSRV on all sub-crates (#146)
• Better CI (#98)
• add missing environment variable options
• remove unnecessary default column for environment variables, surround environment variables in backticks.
• reword resolvers description
• clarify how the resolvers work
• reword usage string
• remove duplicate config module
• Merge branch 'main' of https://github.com/umccr/htsget-rs into more-flexible-config-rename
• fix feature flag compile errors
• add test for long resolvers from environment variable config
• fix broken data server optional by introducing boolean flag to enable data server
• add documentation for reworked config
• flatten data server config
• clippy and fmt
• update config file with default values, add option to print a default config
• allow specifying tags, reference names, fields with an 'All' value
• remove setters, add constructors, add documentation.
• reduce some options for cors, remove repeated code when configuring cors
• fix tests affected by config, change some default values and move around config options
• remove custom deserializer for None option and instead use custom enum
• fix logic involving allowed attributes
• apply changes to other crates from reworked config
• update getter return types
• deserialize empty string as None value
• add cors tests and environment variable tests
• remove public fields, add public getters
• allow configuring multiple data servers
• add expose headers cors option
• move cors config to separate file
• add case insensitive aliases to enum variants
• add allow origins, and separate out tagged and untagged enum variants
• add generic allow type configuration option for allow headers and allow methods
• add cors max age option
• add cors allow header types for cors config
• add CorsConfig shared struct
• add UrlResolver, separate data server config from resolver
• fix errors relating to new config
• use figment instead of config because it is simpler to set defaults
• move config into separate module
• add tests for checking for contained value in interval
• implement query matcher logic
• move fields, tags, no tags, query, and interval to config
• add separate config for local server and s3 storage
• add config file from command line or env option
• swap out envy for config dependency
• Add documentation for cors
• Implement configurable origin for cors
• Add cors allow credentials option to data server config
• Move data server config to separate struct
• Move server config into separate struct
• Implement cors for htsget-http-actix.
• Add more spans and tracing calls.
• Move tracing setup to config.
• Bump dependencies, fix clippy warnings.
• Improve errors so that they are more informative.
• Update README instructions.
• Add ticker server addr test.
• Clean up code, format, update dependencies.
• Implement non-tls ticket server alongside tls ticket server.
• Fix localstorage path (#86)
• Fix tests and errors (#83)
• Deploy htsget-http-lambda. (#81)
• Enable choosing between storage types. (#80)
• Remove file from localstorage (#79)
• Htsget http lambda (#76)