Callnote 歷史舊版本 Page3

更新時間：2021-06-30
更新細節：

What's new in this version:

- [Filesystem] Workaround cannot dumpFile into "protected" folders on Windows
- [Messenger] fix FlattenExceptionNormalizer
- [SecurityBundle] Change information label from red to yellow
- [HttpKernel] Keep max lifetime also when part of the responses don't set it
- [ErrorHandler] fix handling buffered SilencedErrorContext
- [HttpClient] fix Psr18Client when allow_url_fopen=0
- [DependencyInjection] Add support of PHP enumerations
- [Config] fix tracking default values that reference the parent class
- [DependencyInjection] Fix binding "iterable $foo" when using the PHP-DSL
- [Uid] Fix fromString() with low base58 values
- [Cache] handle prefixed redis connections when clearing pools
- [Cache] fix eventual consistency when using RedisTagAwareAdapter with a cluster
- [Cache] Disable locking on Windows by default
- [Mailer] fix encoding of addresses using SmtpTransport
- [HttpKernel] [HttpCache] Keep s-maxage=0 from ESI sub-responses
- Avoid broken action URL in text notification mail
- [VarDumper] Fix tests for PHP 8.1
- [FrameworkBundle] Replace var_export with VarExporter to use array short syntax in secrets list files
- [DependencyInjection] throw proper exception when decorating a synthetic service
- [ErrorHandler] [DebugClassLoader] Do not check Phake mocks classes
- [PhpUnitBridge] fix handling the COMPOSER_BINARY env var when using simple-phpunit
- [HttpFoundation] allow savePath of NativeFileSessionHandler to be null
- [Messenger] prevent reflection usages when classes do not exist
- [Messenger] Remove TLS related options when not using TLS
- [FrameworkBundle] fix Could not find service "test.service_container"
- [HttpClient] fix compat with cURL <= 7.37
- [HttpClient] throw exception when AsyncDecoratorTrait gets an already consumed response
- [Config] fix tracking attributes in ReflectionClassResource
- [Process] Fix incorrect parameter type
- [HttpClient] Revert bindto workaround for unaffected PHP versions
- [Security] Fix opcache preload with alias classes
- [Serializer] Do not allow to denormalize string with spaces only to valid a DateTime object
- [DependencyInjection] Update loader’s directory when calling ContainerConfigurator::withPath
- [FrameworkBundle] fix KernelBrowser::loginUser with a stateless firewall
- [SecurityBundle] Link UserProviderListener to correct firewall dispatcher
- [Console] Escape synopsis output
- [HttpFoundation] Add ReturnTypeWillChange to SessionHandlers

更新時間：2021-06-17
更新細節：

What's new in this version:

Fixed:
security #cve-2021-32693 [SecurityHttp] Fix "Authentication granted with multiple firewalls"
- [Uid] fix performance and prevent collisions with the real clock_seq
- [Security] Fix deprecation notice on TokenInterface::getUser() stringable return
- [Security] Restore extension point in MessageDigestPasswordEncoder
- [Messenger] Fix RequestContext not updated
- [Messenger] Remove TLS related options when not using TLS
- [FrameworkBundle] fix Could not find service "test.service_container"
- [Console] Fix using #[AsCommand] without DI
- [DependencyInjection] fix parsing classes for attributes
- [Runtime] fix overriding --env|-e with single-command apps
- [HttpClient] fix compat with cURL <= 7.37
- [Console] fix managing signals when commands are lazy loaded
- [PasswordHasher] Fix missing PasswordHasherAwareInterface allowed type
- [HttpClient] throw exception when AsyncDecoratorTrait gets an already consumed response
- [Notifier] Escape . char for Telegram transport
- [Config] fix tracking attributes in ReflectionClassResource
- [Process] Fix incorrect parameter type
- [HttpClient] Revert bindto workaround for unaffected PHP versions
- [DependencyInjection] fix [email protected]{env} inside imported files
- [Messenger] fix BC for FrameworkBundle 4.4 with a non-existence alias being used
- Fix not null get collection key types
- [PasswordHasher] Prevent PHP fatal error when using auto algorithm
- [Security] Fix opcache preload with alias classes
- [Serializer] Do not allow to denormalize string with spaces only to valid a DateTime object
- [Console] Fix negated options not accessible
- [Validator] remove service if its class doesn't exist
- [DependencyInjection] Update loader’s directory when calling ContainerConfigurator::withPath
- [FrameworkBundle] fix KernelBrowser::loginUser with a stateless firewall
- [SecurityBundle] Link UserProviderListener to correct firewall dispatcher
- [Console] Escape synopsis output
- [Notifier] [Bridge] Remove hidden dependency on HttpFoundation for SmsBiurasTransport
- Relax requirement on symfony/runtime

更新時間：2021-06-09
更新細節：

What's new in this version:

Fixed:
- Ensured retention of unchanged alignment name and omission of name controls when using the "Replace" option when redoing an alignment
- Fixed an issue where File → Save did not work after redoing an unsaved alignment
- Preserved the display of preferred codons when switching between DNA and mRNA formats when viewing a codon usage table
- Allocated sufficient space to display the "Size" column in Features view when viewing ssDNA and ssRNA sequences
- Prohibited pasting when multiple files are selected in a collection
- Prevented a crash that would occur after double-clicking when importing SnapGene and Addgene online sequences
- Completely removed the installation folder when uninstalling on Windows
- Enabled "File → Export → Alignment..." and "File → Export → Consensus..." when viewing an alignment
- Made significant stability improvements
- Reduced memory usage
- Improved date formatting on Windows
- Improved button placement in History view
- Fixed an issue that could cause custom common features to be corrupted by using the right-click context menu to edit a common feature
- Removed the "Hybridization Parameters" menu action when viewing an RNA sequence in a collection
- Improved manual adjustment of vertical scaling of sequences traces aligned to a reference sequence
- Fixed an issue that prevented importing from Vector NTI databases on Windows
- Addressed an issue with importing some Vector NTI Express databases
- Fixed an issue in which the text representation of History view did not always refresh immediately when edits were made or undone
- Ensured correct enabling and disabling of the "Edit History" control in History view when the history is modified
- Corrected an issue that allowed duplicate primers with the same name but different sequence case to be imported into a file
- Corrected various issues that could occur when attempting to add features to the common features database, or importing such features, if they were marked as not visible in the original document
- Ensured correct export of common features to the specified folder
- Addressed issues that prevented collections stored on Windows network shares from being listed as recent collections in the File → Open Collection menu
- Improved fonts and text placement in History view
- Improved the message shown if an alignment is selected in a collection
- Corrected an issue that could cause pop-up menus to remain open when the Launch dialog was closed
- Corrected an issue that prevented saving a new file created from a selection from being saved to an open collection
- Ensured remembering of a preference for showing additional binding sites that do not match at the 3' end
- Corrected a regression that prevented imported primers from being restricted to those that have a unique binding site
- Ensured that the chosen enzyme set and enzyme visibility are retained when undoing sequence edits.
- Ensured that bold is correctly used to highlight unique cutters after undoing sequence edits
- Reduced the file size when exporting maps and history as PNG images
- Improved the toggling of enzyme visibility when repeatedly clicking check boxes in Enzymes view
- Fixed an issue that prevented looking up an enzyme by right-clicking in the Enzyme or Sites column in Enzymes view
- Fixed an issue that incorrectly suggested a sequence trace has unsaved edits after using File → Save As

更新時間：2021-06-02
更新細節：

What's new in this version:

Fixed:
- [Serializer][Validator] Fix not null return from "getCollectionValueTypes"
- [Security] Readd deprecated methods to the interfaces
- [HttpFoundation] Add ReturnTypeWillChange to SessionHandlers
- [HttpKernel] fix ArgumentMetadataFactory messes up controller arguments with attributes
- Fix Symfony 5.3 end of maintenance date

更新時間：2021-06-01
更新細節：

What's new in this version:

Fixed:
- [Form] Use !isset for checks cause this doesn't falsely include 0
- [DependencyInjection] keep container.service_subscriber tag on the decorated definition
- [Filesystem] fix readlink() for Window
- [Form] fix support for years outside of the 32b range on x86 arch
- Make Mailgun Header compatible with other Bridges
- [Messenger] Fix merging PrototypedArrayNode associative values
- [WebProfilerBundle] Wrapping exception js in Sfjs check and also loading base_js Sfjs if needed
- [VarDumper] Don't pass null to parse_url()

更新時間：2021-05-31
更新細節：

What's new in this version:

- [FrameworkBundle] fix ConfigBuilderCacheWarmer
- [FrameworkBundle] fix creating ContainerBuilder at warmup/CLI time
- [FrameworkBundle] Remove redundant cache service
- [Translation] Remove PoEditor Provider
- [Form] Use !isset for checks cause this doesn't falsely include 0
- [DependencyInjection] keep container.service_subscriber tag on the decorated definition
- [Filesystem] fix readlink() for Windows
- [HttpKernel] Throw when HttpKernel is created and the env is empty
- [SecurityBundle] Don't register deprecated listeners with authenticator manager enabled
- [Form] fix support for years outside of the 32b range on x86 arch
- Make Mailgun Header compatible with other Bridges
- [Messenger] Fix merging PrototypedArrayNode associative values
- [Ldap] Avoid calling the deprecated getUsername()
- [WebProfilerBundle] Wrapping exception js in Sfjs check and also loading base_js Sfjs if needed
- [VarDumper] Don't pass null to parse_url()

更新時間：2021-05-19
更新細節：

What's new in this version:

- security [SecurityCore] Fix user enumeration via response body on invalid credentials
- Fixes Undefined method call
- [SecurityBundle] Remove invalid unused service
- [Security] [DataCollector] Remove allows anonymous information in datacollector
- [FrameworkBundle][Validator] Fix deprecations from Doctrine Annotations+Cache
- [Mailer] Fix SES API call with UTF-8 Addresses
- Fixed deprecation warnings about passing null as parameter
- [Finder] Fix gitignore regex build with "**"
- [HttpClient] fix adding query string to relative URLs with scoped clients
- [DependencyInjection][ProxyManagerBridge] Don't call class_exists() on null
- [Notifier] Add missing charset to content-type for Slack notifier
- [Console] Fix Windows code page support

更新時間：2021-05-14
更新細節：

What's new in this version:

New Functionality:
- Added support for viewing features in multiple sequence alignments
- Enhanced History view with a Text format tab, and with an option to show the entire history
- Added support for RNA sequences as .rna files
- Enabled viewing files of all types simultaneously in a Collection using a new "All Files" area
- Enabled gaps to be displayed every 10th base for protein sequences, and every 10th or 3rd base for nucleotide sequences
- Added support for filling in DNA ends of annealed oligos to create a double-stranded DNA sequence
- Added support for annotating primers that anneal at the 5’ end but not the 3’ end
- Enabled viewing and printing chromatogram files in a wrapped multi-line format
- Improved the conversion of .geneious nucleotide and protein sequences and alignments
- Added DNA Ladders from Ecogen, TIANGEN, and Vazyme

Enhancements:
- Extended the range for the minimum required 3' match for primers from 25 to 35 bases
- Enabled export of alignments to rich text format .rtf files
- Enhanced the visualization of mutagenesis simulations and mutagenic primers
- Enhanced the response to mousing over a primer so that the binding site is now highlighted in gray
- Added support for /protein_id qualifiers for mat_peptide features
- Enabled printing to PDF on macOS when no printers are installed
- Added an indicator in the selection bar to show "DNA" or "RNA" as the sequence type
- Enhanced enzyme, feature, and primer label layout in Map view for linear sequences
- Added clickable "contact support" links to messages that pop up in various places
- Made terminator features directional in the common features database
- Added the keyboard shortcuts Cmd+1 / Cmd+2 / Cmd+3 for switching between tabs in chromatogram windows
- Enhanced cursor placement, highlighting, and trace data tooltips when the mouse cursor is between bases
- Changed the "Replace" button label in Collections to "Bulk Edit" for improved clarity and accuracy
- Improved primer binding sites to avoid bulges if a 5' N tail is present in the primer sequence
- Updated the MAFFT aligner to version 7.471
- Updated the Parasail aligner to version 2.4.2
- Added a shortcut (Shift + Spacebar) for scrolling one page up in multiple sequence alignments
- Streamlined toolbar on macOS

Fixed:
- Rationalized the View menu to show options relevant to the file type
- Removed the "Browse..." menu action that had no effect in the "Import Primers from a SnapGene File" dialog
- Adjusted the tooltips for buttons in the "Find" bar to make them more consistent with other tooltips
- Changed the heading in the Collection search dialog for Protein Files to say "Names" rather than "Names & Numbers"
- Ensured that only a single /mod_base qualifier is allowed for modified_base features
- Added a ruler for protein sequences when viewing in compact format
- Fixed a bug with selection of the last item in Features, Primers, and Enzymes views
- Implemented immediate update of the version listed on the account administrator page after SnapGene is updated
- Corrected a regression in which sequence selection was lost after clicking in the Description Panel
- Corrected a regression with enzyme site selection in Lines mode of Enzymes view
- Ensured consistent display of the selection when switching to Sequence view
- Fixed an issue in which spaces were not shown after commas on macOS Big Sur
- Fixed a non-functional "Choose Enzymes..." command in the "Choose enzyme set" dropdown menu
- Corrected a regression that caused overtyping of characters in the primer name fields of the Simulate Agarose Gel dialog
- Ensured correct refreshing of primer binding sites when changing hybridization parameters
- Prevented truncation of 3' overhangs that extend beyond the end of a circular sequence
- Prevented input of an invalid location in the Go To dialog for sequences aligned to a reference DNA sequence
- Fixed some tabs that displayed as white text on a white background on macOS Big Sur
- Ensured that features are not lost from inserts in cloning operations when windows are opened or closed
- Corrected the color of the gray bar below the list box in the Collection interface
- Prevented "< Please choose >" from being propagated from the Anneal Oligos dialog to the oligo names in the resulting history
- Ensured that in the Anneal Oligos dialog, a double-click on a compatible enzyme is needed to transfer focus to the Restriction Enzymes dialog
- Configured the pull-down menus in the Anneal Oligos dialog to refresh when documents are opened or closed
- Ensured that the specified font size is used when printing the Description Panel
- Fixed an issue with the folder location used when exporting standard common features
- Improved scrolling performance in Enzymes view
- Fixed the default file name chosen when exporting a single file from a Collection
- Improved the reliability of displaying the warning in the Print dialog on Windows about printing to PDF
- Ensured that tabbed window controls on macOS are reliably shown
- Improved the background color display in Map view
- Fixed issue in which keywords could be used as the construct name for some GenBank/GenPept files
- Improved the opening of SeqBuilder files
- Addressed issues with importing references from another file
- Improved the quality when exporting maps at high resolutions
- Updated Map, Sequence, and other views when protein sequences are zoomed
- Implemented hiding of zoom controls in a collection when switching from a long sequence that supports zooming to a shorter one that does not
- Prevented unnecessary display of a message about unsupported qualifiers during NCBI import when the content includes nonstandard qualifiers (e.g., /UniProtKB_evidence) that are deliberately converted to /note qualifiers
- Corrected an issue in which some line breaks in /note qualifiers were not preserved when opening GenBank or GenPept files
- Addressed a potential stability issue when viewing protein files
- Fixed copying of maps and histories on macOS, and improved the quality when pasting such content into applications such as Microsoft Word or PowerPoint on macOS
- Improved the message shown when attempting to use a sequence over 1 Mbp to compute a pairwise alignment
- Ensured correct identification of macOS Big Sur when sending anonymous user statistics
- Ensured correct display of a trace file icon in the Windows menu
- Fixed various issues with specifying and displaying the /collection_date qualifier
- Addressed an issue that could result in sequence characters moving slightly after periods of no mouse activity on Windows and Linux
- Simplified the choice of a destination folder during import into a collection by making the "Add" button the default
- Improved the display of feature names on Windows during pliancy and selection
- Fixed the Redo shortcut on Linux
- Improved margins and alignment in various windows and dialogs
- Improved the default placement of a window created via File → Open when no document was previously open
- Improved stability while viewing collections
- Avoided duplication of DNA documents in the Window menu after converting to single- or double-stranded format
- Corrected the shortcut for Overlap Extension PCR of two fragments
- Ensured that if the side toolbar button is used to show alignments and there are no currently aligned sequences, the software asks which files to import to align to the reference sequence
- Corrected an issue in which unmodified alignment documents sometimes indicated unsaved changes
- Corrected issues with dragging collection files onto other applications
- Fixed a crash when saving an alignment to a collection
- Disabled "Actions → Convert to Single-Stranded..." when viewing alignments
- Corrected an issue that prevented conversion of a feature translation to upper- or lowercase if the last selected codon was located at the end of the sequence
- Fixed a bug in which an open document might not be listed in the Window menu or in the lists of open documents in cloning dialogs, while the launch dialog would remain visible
- Fixed an issue that could result in two copies of the application running on macOS
- Ensured correct rendering of multi-region Site features that span multiple rows in Sequence view
- Addressed a stability issue when exporting and opening the alignment consensus
- Removed the dead "Browse..." action in the source menu when importing features from BED, GFF3, or GTF files
- Ensured that "Primers → Sort Primer List..." executes the desired sort
- Updated outdated web links to online resources
- Ensured correct residue numbering for Smith-Waterman (local) pairwise alignments

更新時間：2021-05-12
更新細節：

What's new in this version:

- security #cve-2021-21424 [Security][Guard] Prevent user enumeration
- [DependencyInjection] fix dumping service-closure-arguments
- [Console] Fix Windows code page support
- [Security] Make Login Rate Limiter also case insensitive for non-ascii user identifiers
- WDT: Only load "Sfjs" if it is not present already
- [Inflector][String] wrong plural form of words ending by "pectus"
- [HttpClient] Don't prepare the request in ScopingHttpClient
- [Security] Make Login Rate Limiter case insensitive
- [Security] Reset limiters on successful login
- [Security] NullToken signature
- Fix/Rewrite .gitignore regex builder
- [Console] Fix Windows code page support
- [Security] Allow ips parameter in access_control to accept comma-separated string
- [TwigBridge] Fix HTML for translatable custom-file label in Bootstrap 4 theme
- [Notifier] [Bridge] Fix missed messageId for SendMessage object in slack notifier
- [PropertyInfo] PhpDocExtractor: Handle "true" and "false" property types
- [Form] Add missing TranslatableMessage support to choice_label option of ChoiceType
- [Config][DependencyInjection] Uniformize trailing slash handling
- [PropertyInfo] Make ReflectionExtractor correctly extract nullability
- [PropertyInfo] fix attribute namespace with recursive traits
- [PhpUnitBridge] Fix tests with @doesNotPerformAssertions annotations
- [Cache] Check if phpredis version is compatible with stream parameter
- [Notifier] Fix return SentMessage then Messenger not used
- [VarExporter] Add support of PHP enumerations
- Fix return type in isAllowedProperty method on ReflectionExtractor class
- [Notifier] Make FailoverTransport always pick the first transport
- [Inflector][String] Fixed singularize edges > edge
- [ErrorHandler] Skip "same vendor" @method deprecations for Symfony* classes unless symfony/symfony is being tested

更新時間：2021-05-02
更新細節：

What's new in this version:

- [Security] Do not try to rehash null-passwords
- [Security] [Security/Core] fix checking for bcrypt
- [Yaml] expose references detected in inline notation structures
- [HttpFoundation] Fixes for PHP 8.1 deprecations
- [Mailer] use correct spelling when accessing the SMTP php.ini value
- [Yaml] Allow tabs as separators between tokens
- [Cache] phpredis: Added full TLS support for RedisCluster
- [DependencyInjection] [AliasDeprecatedPublicServicesPass] Noop when the service is private
- [FrameworkBundle] Fix array controller link in debug:router
- [DoctrineBridge] Add support for a driver type "attribute"
- RequestMatcher issue when _controller is a closure
- [PropertyInfo] Use the right context for methods defined in traits
- [WebProfilerBundle] Use ControllerReference instead of URL in twig render()
- [SecurityBundle] Empty line starting with dash under "access_control" causes all rules to be skipped
- [Cache] Apply NullAdapter as Null Object
- [Cache][FrameworkBundle] Fix logging for TagAwareAdapter
- [Routing] Better inline requirements and defaults parsing
- [PhpUnitBridge] Fix phpunit symlink on Windows
- [Form] Fix 'invalid_message' use in multiple ChoiceType
- [Yaml] Fixed infinite loop when parser goes through an additional and invalid closing tag
- [Console] Add Helper::width() and Helper::length()
- [Debug][ErrorHandler] Avoid warning with Xdebug 3 with develop mode disabled
- [HttpClient] allow CurlHttpClient on Windows
- [Yaml] fix parsing some block sequences
- Fixed bugs found by psalm
- [Config] Fixed support for nodes not extending BaseNode
- [RateLimiter] Fix sleep value
- [FrameworkBundle] Dont store cache misses on warmup
- [DependencyInjection] Fix "url" env var processor behavior when the url has no path
- [Cache] skip storing failure-to-save as misses in ArrayAdapter
- [Serializer] Allow AbstractNormalizer to use null for non-optional nullable constructor parameters without default value
- add missing queue_name to find(id) in doctrine messenger transport
- [FrameworkBundle] dont access the container to configure http_cache