NEWS

CHANGES IN VERSION 3.99.0
----------------------

MAJOR UPDATES

    o 3.99.0 Update downloading method from httr to httr2

BUG CORRECTION

    o 3.99.1 Fix bug preventing status message with removeResource
    o 3.99.2 Add ability to pass a config argument to download resources
    o 3.99.3 Add ability to pass a progress argument to download resources


CHANGES IN VERSION 3.13.0
-------------------------

BUG CORRECTION

    o (3.13.1) merged @votti PR for not checking connection if localhub is selected

NEW FEATURES

    o (3.13.2) Add auto clean of cache if corrupt index file
    o (3.13.3) Add auto redownload once if resource is not loading in R, if localHub
    is not selected and internet available. 

CHANGES IN VERSION 3.11.0
-------------------------

BUG CORRECTION

    o (3.11.4) Correct subsetting. Didn't account for multiple files associated
    with single entry (ie. bam/bai).

CHANGES IN VERSION 3.9.0
-------------------------

NEW FEATURES

    o (3.9.1) Remove the defunct `display` method for AnnotationHub.
    o (3.9.1) Rename vignette from TroubleshootingTheCache to TroubleshootingTheHubs
    
CHANGES IN VERSION 3.7.0
-------------------------

NEW FEATURES

     o (3.7.4) Suppress snapshot date unless interactive session 
     o (3.7.1) Add DispatchClass for keras model weights

DEPRECATED

    o (3.7.2) Deprecate display in favor of BiocHubsShiny; see vignette


CHANGES IN VERSION 3.5.0
-------------------------

NEW FEATURES

    o (3.5.2) Add dcf dispatchclass
    o (3.5.1) Add CompDb dispatchclass


CHANGES IN VERSION 3.3.0
-------------------------

NEW FEATURES

    o (3.3.6) Serialized S4 hub resources (AnnotationHub and ExperimentHub)
      are now passed thru updateObject() at load-time

USER-VISIBLE MODIFICATIONS

    o (3.3.8) Add instructions for creating a hub shared across multiple users
    o (3.3.2) Remove TESTING option as only needed to expose devel orgdb
    o (3.3.2) Change filter for orgdbs. orgdbs at release time will be stamped
    with devel (to be release) and then manually have biocversion added for the
    upcoming new devel. Filtering then based on biocversion number. This will
    expose devel orgdbs as soon as generated
    
BUG CORRECTION

    o (3.1.9) Fix broken test. Identical not appropriate. all present appropriate
    
CHANGES IN VERSION 3.1.0
-------------------------

MAJOR UPDATES

    o (3.1.2) In accordance with the deprecated caching location, upgraded to
    error/defunct from warning/deprecated in preparaion for removal of
    dependency next release


USER-VISIBLE MODIFICATIONS

    o (3.1.1) If there is a duplicate entry in the hub cache for a resource, hub
    code will no longer produce an ERROR. If the duplicate resource was not
    requested the duplicate is ignored. If the duplicate resource is requested,
    produce a warning for corrupt cache and continue with first found entry.
    o (3.1.3) Fix typo in message display 
    o (3.1.5) Deprecate the `display,Hub-method`

BUG CORRECTION

    o (3.1.7) Fix ERROR message for out-dated orgDbs 


CHANGES IN VERSION 2.99.0
-------------------------

MAJOR UPDATES

    o (2.99.0) The default caching location has changed. Instead of
    rappdirs::user_cache_dir using tools::R_user_dir. To avoid conflicting
    caches, a user will have to manage an old cache location before
    proceeding. Information for handling an old cache location is provided in
    the vignette.
    o (2.99.0) Another major change, a default caching location is automatically
    created in a non interactive session instead of using a temporary
    location. In an interactive session, a user is still prompted for
    permission.

CHANGES IN VERSION 2.23.0
-------------------------

USER-VISIBLE MODIFICATIONS

    o (2.23.2) Create a new all encompassing vignette that references both
    ExpeirmentHub and AnnotationHub. Reference this one vignette in all four
    related packages instead of trying to maintain multiple vigenttes that were
    essentially the same. This also involves removing CreateAnAnnotationPackage
    
MODIFICATIONS

    o (2.23.1) Fixed ERROR message to better indicate vignette troubleshooting
    document and fixed reference in Troubleshooting vignette. These ERRORs are
    triggered by both AnnotationHub and ExperimentHub so clarified the
    Troubleshooting document is in AnnotationHub. 

CHANGES IN VERSION 2.21.0
-------------------------
BUG FIX

    o (2.21.5) Fix documentation for setting AnnotationHubOptions
    o (2.21.3) Fix printing of proxy when present
    
USER-VISIBLE MODIFICATIONS

    o (2.21.6) Make internet connection test less stringent
    o (2.21.4) Add link to github for reporting issues
    o (2.21.2) Update to reference hubs@bioconductor.org for help 
    o (2.21.1) Update .tidyGRanges to account for incorrect or missing genomes


CHANGES IN VERSION 2.19.0
-------------------------

BUG FIX

    o (2.19.12) change has_internet to nslookup to avoid locations that do not
    have access to google dns.

NEW FEATURES

    o (2.19.8) Fixed messages to be more informative
    o (2.19.8) trycatch around bfcneedsupdate/bfcdownload for sqlite database to
    prevent error when internet is spotty and databse source cannot be checked
    for a newer version.
    o (2.19.4) trycatch around bfcneedsupdate call will prevent error when
    internet is spotty and resource cannot be checked for a newer version.
    o (2.19.3) New function removeResources for removing locally downloaded
    cached resources. Nicer interface than using cache. Improved documentation
    on use of setting a cache to NULL to also remove resources.
    o (2.19.2) Adds option ask to constructor. Default: True. Ask will ask user
    to create default AnnotationHub location and if in an non interactive
    session utilize a temporary directory. If False, the default directory is
    created and utilized without prompting.

USER-VISIBLE MODIFICATIONS

    o (2.19.1) Improve ERROR message when resource isn't found. Also involved
    updating RecordStatus function. If resource hasn't been completely removed
    from database, gives when the resource was removed. If the resource is
    available but after the snapshot date being utilized, specialized message.

CHANGES IN VERSION 2.17.0
-------------------------

NEW FEATURES

    o (2.17.6) remove debugging message of loading resource (`AH: 1`)
    o (2.17.5) system environment variable to control localHub option for
    creating hub based only on previously downloaded resources
    o (2.17.9) Allow force redownload of Hub sqlite file with refreshHub
    o (2.17.12) Only display download message when something to download.
    o (2.17.13) The output list of files is the AH/EH id not AHid:resourceid

BUG FIXES

    o (2.17.4) Fix localHub when no internet connection.  The internal use of
    isDevel was preventing Hub creation when no internet connection. Fixed by
    checking connection. This code pretained to orgDb filters
    o (2.17.8) On chance of very first download of hub failure, next call to
    construtor will redownload
    o (2.17.10) Fix ability to use hubs when offline
    o (2.17.11) Add BiocVersion to Imports. Fixes bug with R CMD check when
    testing if library can be loaded off search path. BiocManager doesn't Import
    BiocVersions and this is needed to get the correct BiocManager version of
    the snapshot date.

CHANGES IN VERSION 2.15.0
-------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o (2.15.9) The Hubs have been updated to use BiocFileCache as a backend
    utility for managing and downloading resources. This allows for file
    specific caching mechanism. This change is a significant user change as it
    changed the default directories for the Hubs (AnnotationHub/ExperimentHub)
    as well as the base directory no longer being hidden.

NEW FEATURES

    o (2.15.15) Added BamFile Resource method
    o (2.15.9) Add helper function to get additional information on
    resources. getInfoOnIds
    o (2.15.2) Add function to list currently available DispatchClass

USER-VISIBLE MODIFICATIONS

    o (2.15.3)  Bioconductor will no longer accept random, Individual resources
    without an accompanied package.
    o (2.15.4)  We also encourage the use of AnnotationHub rather than very
    large annotation packages. We added sections for users wishing to convert
    existing packages to use AnnotationHub as well.
    o (2.15.7) There were substantial updates to Rsamtools. Rsamtools no longer
    supports razip files. These files have been removed from the hub and
    vignette updated to use the twobit and gff files

BUG FIXES
    o (2.15.5) Fixed bug. If resources are removed from the hub, this should
    only be reflected in the devel branch but still be available in release
    branch. The filter for exposed resources was refined to respect
    datadateremoved


CHANGES IN VERSION 2.12.0
-------------------------

MODIFICATIONS

    o Updated code from BiocInstaller to BiocManager

CHANGES IN VERSION 2.12.0
-------------------------

BUG FIXES

    o Prompt for permission when downloading many (more than
    AnnotationHubOption("MAX_DOWNLOADS")) resources.

MODIFICATIONS

    o Moved readMetadataFromCsv back to AnnotationHubData.

    o Use AnnotationHubData::makeAnnotationHubMetadata to validate metadata.csv

CHANGES IN VERSION 2.10.0
------------------------

NEW FEATURES

    o AnnotationHub will now work offline utilizing argument 'localHub'; will
    also use this option automatically if no internet connection is detected.

    o Added new GDSResource class

    o Added documentation for creating an AnnotationHub package

MODIFICATIONS

    o Modified tags vector when passed to display to improve speed of display
    querying

    o Moved readMetadataFromCsv from AnnotationHubData.

    o Removed listResources and loadResource from AnnotationHub; not implemented
    and only valid in ExperimentHub

BUG FIXES

    o Expose snapshot less than or equal to release date

    o Force rebuild of index if index file corrput or out of date

CHANGES IN VERSION 2.8.0
------------------------

NEW FEATURES

    o add .get1,RDSResource-method

    o add RdsResource class

    o add EnsDb dispatch class

    o expose rdatapath in metadata

MODIFICATIONS

    o modify records exposed as metadata
      - expose records added <= snapshot date
      - expose a single OrgDb per organism per BioC version

    o edits to .get1,GenomicScores-method and .get1,GenomicScoresResource-method

    o work on biocVersion and snapshotDate relationship:
      - snapshotDate() must be <= biocVersion() release date
      - possibleDates() are now filtered by snapshotDate()

    o remove GenomicScoresResource; Robert Castelo will handle loading these
    resources in his GenomicScores software package

    o Changed show method for hub object
      - removed sourcelastmodifieddate
      - added rdatadateadded


BUG FIXES

    o fix bug in ordering of output from .uid0()

    o fix bugs in 'snapshotDate<-' method

CHANGES IN VERSION 2.6.0
------------------------

NEW FEATURES

    o add vignette section on sharing resources on clusters

    o add 'preparerclass' to index.rda to allow search by package name for
      ExperimentHub objects

    o add GenomicScoresResource class for Robert Castelo

MODIFICATIONS

    o return 'tags' metadata as list instead of comma-separated character
      vector

    o move AnnotationHubRecipes vignette to AnnotationHubData

    o move listResources() and loadResources() from ExperimentHub

    o expose additional fields in .DB_RESOURCE_FIELDS()

    o modify cache path to avoid creating a '~' directory on Mac

    o use https: NCBI rul in documentation

    o modify .get1,EpiExpressionTextResource-method to use 'gene_id'
      column as row names


CHANGES IN VERSION 2.4.0
------------------------

NEW FEATURES

    o add new status codes '4' and '5' to 'statuses' mysql table;
      change 'status_id' field to '4' for all removed records to date

    o add getRecordStatus() generic

    o add package() generic

    o create 'Hub' VIRTUAL class
      - add new .Hub() base constructor for all hubs
      - add getAnnotationHubOption() and setAnnotationHubOption()
      - promote cache() to generic
      - add getHub() getter for AnnotationHubResource class
      - add getUrl(), getCache(), getDate() getters
      - export as few db helpers as possible

    o add 'EpigenomeRoadmapNarrowAllPeaks' and
      'EpigenomeRoadmapNarrowFDR' classes

MODIFICATIONS

    o distinguish between broad and narrow peak files in
      EpigenomeRoadmapFileResource dispatch class

    o don't use cache for AnnotationHub SQLite connection
      - originally introduced so could be closed if needed, but
	creates complexity
      - instead, open / close connection around individual queries (not a
	performance concern)
      - expose hub, cache, proxy in AnnotationHub constructor
      - document dbconn,Hub-method, dbfile,Hub-method, .db_close

    o snapshotDate now uses timestamp (last date any row was modified) instead
      of rdatadateadded

    o .require fails rather than emits warning
      - unit test on .require()
      - also, cache(hub[FALSE]) does not create spurious error

    o work on removed records and biocVersion
      - .uid0() was reorganized and no longer groups by record_id
      - metadata is returned for records with
	biocversion field <= current biocVersion
	instead of an exact match with the current version
      - metadata is not returned for removed records

BUG FIXES

    o Work around httr() progress() bug by disabling progress bar


CHANGES IN VERSION 2.2.0
------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o seqinfo(GRanges) for all genomes supported by GenomeInfoDb now
      contain seqlengths.


CHANGES IN VERSION 2.1.21
--------------------------

SIGNIFICANT USER-VISIBLE CHANGES

    o fileName() returns the cache path on the disk for a file that
      has been cached and NA for files which have not been cached.

    o The error message (when file is not downloaded from the hub)
      displays the AnnotationHub name, title, and reason for failure.


CHANGES IN VERSION 2.1
----------------------

NEW FEATURES

    o as.list() splits AnnotationHub instances into a list of
    instances, each with a single record. c() concatenates hubs.

BUG FIXES

    o cache<- now behaves as documented, e.g., removing the cached
    version of the file.

CHANGES IN VERSION 2.0.0
------------------------

NEW FEATURES

    o AnnotationHub is all new.  We basically rewrote the entire thing.

    o The back end is new (new database, new way of tracking/routing
    data etc.)

    o The front end is new (new AnnotationHub object, new methods, new
    behaviors, new ways of finding and downloading data)

    o The metadata has also been cleaned up and made more
    consistent/searchable

    o The recipes that are used to populate these data have also been
    cleaned up.

    o There is also a new vignette to explain how to use the new
    AnnotationHub in detail

IMPROVEMENTS SINCE LAST TIME

    o The old way of finding data (an enormous tree of paths), was not
    really scalable to the amount of data we have to provide access
    to.  So we junked it.  Now you have a number of better methods to
    allow you to search for terms instead.

    o The new hub interface can be searched using a new display
    method, but it can *also* be searched entirely from the command
    line.  This allows you to use it in examples and scripts in a way
    that is friendlier for reproducible research.

    o For users who want to contribute valuable new annotation
    resources to the AnnotationHub, it is now possible to write a
    recipe and test that it works for yourself.  Then once you are
    happy with it, you can contact us and we can add data to the
    AnnotationHub.