Gatekeeper is used to track the production and validation of batches of tag plates for sequencing. It is designed to interface with the Sequencescape LIMS.
🚨 Your current dependencies have known security vulnerabilities 🚨
This dependency update fixes known security vulnerabilities. Please see the details below and assess their impact carefully. We recommend to merge and deploy this as soon as possible!
Here is everything you need to know about this update. Please take a good look at what changed and the test results before merging this pull request.
There is a possible ReDoS vulnerability in the block_format helper in Action Mailer. This vulnerability has been assigned the CVE identifier CVE-2024-47889.
Impact
Carefully crafted text can cause the block_format helper to take an unexpected amount of time, possibly resulting in a DoS vulnerability. All users running an affected release should either upgrade or apply the relevant patch immediately.
Ruby 3.2 has mitigations for this problem, so Rails applications using Ruby 3.2 or newer are unaffected. Rails 8.0.0.beta1 requires Ruby 3.2 or greater so is unaffected.
Releases
The fixed releases are available at the normal locations.
Workarounds
Users can avoid calling the block_format helper or upgrade to Ruby 3.2
There is a possible ReDoS vulnerability in Action Controller's HTTP Token authentication. This vulnerability has been assigned the CVE identifier CVE-2024-47887.
Impact
For applications using HTTP Token authentication via authenticate_or_request_with_http_token or similar, a carefully crafted header may cause header parsing to take an unexpected amount of time, possibly resulting in a DoS vulnerability. All users running an affected release should either upgrade or apply the relevant patch immediately.
Ruby 3.2 has mitigations for this problem, so Rails applications using Ruby 3.2 or newer are unaffected. Rails 8.0.0.beta1 depends on Ruby 3.2 or greater so is unaffected.
Releases
The fixed releases are available at the normal locations.
There is a possible ReDoS vulnerability in the query parameter filtering routines of Action Dispatch. This vulnerability has been assigned the CVE identifier CVE-2024-41128.
Impact
Carefully crafted query parameters can cause query parameter filtering to take an unexpected amount of time, possibly resulting in a DoS vulnerability. All users running an affected release should either upgrade or apply the relevant patch immediately.
Ruby 3.2 has mitigations for this problem, so Rails applications using Ruby 3.2 or newer are unaffected. Rails 8.0.0.beta1 depends on Ruby 3.2 or greater so is unaffected.
Releases
The fixed releases are available at the normal locations.
There is a possible ReDoS vulnerability in the plain_text_for_blockquote_node helper in Action Text. This vulnerability has been assigned the CVE identifier CVE-2024-47888.
Impact
Carefully crafted text can cause the plain_text_for_blockquote_node helper to take an unexpected amount of time, possibly resulting in a DoS vulnerability. All users running an affected release should either upgrade or apply the relevant patch immediately.
Ruby 3.2 has mitigations for this problem, so Rails applications using Ruby 3.2 or newer are unaffected. Rails 8.0.0.beta1 depends on Ruby 3.2 or greater so is unaffected.
Releases
The fixed releases are available at the normal locations.
Workarounds
Users can avoid calling plain_text_for_blockquote_node or upgrade to Ruby 3.2
💥 Drop ruby 2.7 and 3.0 support, and require ruby 3.1 by @nevans in #276
💥⚡ Simplify header-fld-name parser (backward incompatible) by @nevans in #216
For example, HEADER.FIELDS(Content-Type) or HEADER.FIELDS("Content-Type") are semantically identical, and a server may choose to return the quoted version.
Before this change, the FetchData attr header name would be quoted if the server sent the field name quoted.
After this change, the header field names will always be unquoted by the parser, so the result will always available via fetch_data.header_fields("Content-Type") or fetch_data.attr_upcase["HEADER.FIELDS(CONTENT-TYPE)"].
💥 Replace MessageSet with SequenceSet by @nevans in #282
Most of the changes are bugfixes or allow something new to work that didn't work before. See the PR for more details.
This affects #search, #uid_search, #sort, #uid_sort, #fetch, #uid_fetch, #store, #uid_store, #copy, #uid_copy, #move, #uid_move, and #uid_expunge.
💥 SequenceSet input validation for Set, Array, and enumerables by @nevans in #319
Array inputs can still be deeply nested.
Set inputs can only contain integers and "*" or :*, to be consistent with SequenceSet#to_set.
Other Enumerables will only be converted if they implement #to_sequence_set.
🔥 Remove deprecated #client_thread attr_reader by @nevans in #321 #client_thread was deprecated by v0.4.0.
🔥 Drop deprecated BodyType structs by @nevans in #323 These structs were deprecated by v0.4.0.
Added
✨ Add #extract_responses method by @nevans in #330Also backported to v0.4.17.
✨ New config option to return frozen dup from #responses by @nevans in #334Also backported to v0.4.17.
🥅 Improve SequenceSet frozen errors by @nevans in #331Also backported to v0.4.17.
📚 SequenceSet API is considered stable now by @nevans in #318
🔒 Enforce LOGINDISABLED requirement by @nevans in #307
To workaround buggy servers, config.enforce_logindisabled can be set to :when_capabilities_cached or false.
🔒 SASL DIGEST-MD5: realm, host, service_name, etc by @nevans in #284 Please note that the DIGEST-MD5 SASL mechanism is insecure and deprecated.
Deprecations
🔊 Warn about deprecated #responses usage by @nevans in #97
To silence these warnings:
pass a block to #responses(supported since v0.4.0),
pass a response type to #responses for a frozen copied array (since v0.4.17),
set config.responses_without_block to :silence_deprecation_warning(since v0.4.13),
set config.responses_without_block to :frozen_dup for a frozen copy (since v0.4.17),
use #clear_responses instead (since v0.4.0),
use #extract_responses instead (since v0.4.17).
🗑️ Deprecate MessageSet by @nevans in #282 MessageSet was only intended for internal use, and all internal usage has been replaced.
Fixed
🐛 Fix #send_data to send DateTime as time by @taku0 in #313 Also backported to v0.4.15.
🐛 Fix #header_fld_name to handle quoted strings correctly by @taku0 in #315 Also backported to v0.4.16.
🐛 Fix SequenceSet[input] when input is a SequenceSet by @nevans in #326 Also backported to v0.4.17.
🐛 Fix Set inputs for SequenceSet by @nevans in #332 This bug was introduced by #319, which had not been previously released.
Other Changes
🔧 Update default config for v0.5 by @nevans in #305
♻️ Use Integer.try_convert (new in ruby 3.1+) by @nevans in #316
🗑️ Add category: :deprecated to calls to warn by @nevans in #322
♻️ Extract SASL::Authenticators#normalize_name by @nevans in #309
🔒 📚 Improvements and docs for SASL::ClientAdapter by @nevans in #320
worked for most objects, they did not for classes and modules that were also
namespaces (i.e., those defined by a file and matching subdirectories). In
such cases, their child constants could not be autoloaded.
This limitation has been removed.
TracePoint is no longer used.
Requires Ruby 3.2 or later.
Gems that work with previous versions of Zeitwerk also work with this one. If
they support Ruby versions older than 3.2 they can specify a relaxed version
constraint for Zeitwerk like "~> 2.6", for example.
In client projects, Bundler takes the Ruby requirement into account when
resolving dependencies, so Gemfile.lock will get one compatible with the
Ruby version being used.
2.6.18 (from changelog)
Fixes a bug in which projects reopening the main namespace of a gem dependency
managed by its own Zeitwerk loader could not reload the constants they added
to that external namespace.
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🚨 Your current dependencies have known security vulnerabilities 🚨
This dependency update fixes known security vulnerabilities. Please see the details below and assess their impact carefully. We recommend to merge and deploy this as soon as possible!
Here is everything you need to know about this update. Please take a good look at what changed and the test results before merging this pull request.
What changed?
✳️ rails (7.0.8.4 → 7.0.8.6) · Repo
Release Notes
7.0.8.6
7.0.8.5
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Commits
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↗️ actioncable (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ actionmailbox (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
↗️ actionmailer (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Security Advisories 🚨
🚨 Possible ReDoS vulnerability in block_format in Action Mailer
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ actionpack (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Security Advisories 🚨
🚨 Possible ReDoS vulnerability in HTTP Token authentication in Action Controller
🚨 Possible ReDoS vulnerability in query parameter filtering in Action Dispatch
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ actiontext (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Security Advisories 🚨
🚨 Possible ReDoS vulnerability in plain_text_for_blockquote_node in Action Text
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ actionview (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ activejob (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ activemodel (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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↗️ activerecord (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ activestorage (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ activesupport (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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↗️ date (indirect, 3.3.4 → 3.4.0) · Repo
Release Notes
3.4.0
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↗️ loofah (indirect, 2.22.0 → 2.23.1) · Repo · Changelog
Release Notes
2.23.1
2.23.0
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↗️ net-imap (indirect, 0.4.14 → 0.5.1) · Repo
Release Notes
0.5.1
0.5.0
0.4.18
0.4.17
0.4.16
0.4.15
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↗️ nio4r (indirect, 2.7.3 → 2.7.4) · Repo · Changelog
Commits
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↗️ rack (indirect, 2.2.9 → 2.2.10) · Repo · Changelog
Release Notes
2.2.10 (from changelog)
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↗️ railties (indirect, 7.0.8.4 → 7.0.8.6) · Repo · Changelog
Release Notes
7.0.8.6 (from changelog)
7.0.8.5 (from changelog)
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Commits
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↗️ thor (indirect, 1.3.1 → 1.3.2) · Repo · Changelog
Release Notes
1.3.2
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↗️ timeout (indirect, 0.4.1 → 0.4.2) · Repo
Release Notes
0.4.2
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↗️ zeitwerk (indirect, 2.6.17 → 2.7.1) · Repo · Changelog
Release Notes
2.7.1 (from changelog)
2.7.0 (from changelog)
2.6.18 (from changelog)
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