Package 'AnnotationHubData' reference manual

Title:	Transform public data resources into Bioconductor Data Structures
Description:	These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.
Authors:	Martin Morgan [ctb], Marc Carlson [ctb], Dan Tenenbaum [ctb], Sonali Arora [ctb], Paul Shannon [ctb], Lori Shepherd [ctb], Bioconductor Package Maintainer [cre]
Maintainer:	Bioconductor Package Maintainer <[email protected]>
License:	Artistic-2.0
Version:	1.37.0
Built:	2024-11-29 03:40:30 UTC
Source:	https://github.com/bioc/AnnotationHubData

Transform public data resources into Bioconductor Data Structures

Description

These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.

Details

This package provides a set of methods which convert bioinformatic data resources into standard Bioconductor data types. For example, a UCSC genome browser track, expressed as a BED file, is converted into a GRanges object. Not every valuable data resource can be transformed quite so easily; some require more elaborate transformation, and hence a more specialized recipe. Every effort is made to limit the number of recipes required. One strategy that helps with the principle of "zero curation": unless absolutely required, the "cooked" version of the data resource produced by a recipe is a simple and unembellished reflection of the original data in its downloaded form.

Author(s)

Dan Tenenbaum, Paul Shannon

Class `"AnnotationHubMetadata"` and methods

Description

AnnotationHubMetadata is used to represent record(s) in the server data base.

Usage

AnnotationHubMetadata(AnnotationHubRoot, SourceUrl, SourceType,
		 SourceVersion, SourceLastModifiedDate, SourceMd5 =
		 NA_character_, SourceSize, DataProvider, Title,
		 Description, Species, TaxonomyId, Genome, Tags,
		 Recipe, RDataClass, RDataDateAdded, RDataPath,
		 Maintainer, ..., BiocVersion = BiocManager::version(),
		 Coordinate_1_based = TRUE, Notes = NA_character_,
		 DispatchClass, Location_Prefix =
		 "https://bioconductorhubs.blob.core.windows.net/annotationhub/")

toJson(x)
constructSeqInfo(species, genome)

metadata(x, ...)
hubError(x)
inputFiles(object, ...)
outputFile(object)
ahmToJson(ahm)
deleteResources(id)
getImportPreparerClasses()
makeAnnotationHubResource(objName, makeAnnotationHubMetadataFunction,
			  ..., where)
AnnotationHubMetadata(AnnotationHubRoot, SourceUrl, SourceType,
		 SourceVersion, SourceLastModifiedDate, SourceMd5 =
		 NA_character_, SourceSize, DataProvider, Title,
		 Description, Species, TaxonomyId, Genome, Tags,
		 Recipe, RDataClass, RDataDateAdded, RDataPath,
		 Maintainer, ..., BiocVersion = BiocManager::version(),
		 Coordinate_1_based = TRUE, Notes = NA_character_,
		 DispatchClass, Location_Prefix =
		 "https://bioconductorhubs.blob.core.windows.net/annotationhub/")

toJson(x)
constructSeqInfo(species, genome)

metadata(x, ...)
hubError(x)
inputFiles(object, ...)
outputFile(object)
ahmToJson(ahm)
deleteResources(id)
getImportPreparerClasses()
makeAnnotationHubResource(objName, makeAnnotationHubMetadataFunction,
			  ..., where)

Arguments

`AnnotationHubRoot`	`character(1)` Absolute path to directory structure containing resources to be added to AnnotationHub. Internal use only.
`SourceUrl`	`character()` URL of original resource(s).
`SourceType`	`character()` Form of original data, e.g., BED, FASTA, etc. `getValidSourceTypes()` list currently acceptable values. If nothing seems appropiate for your data reach out to [email protected].
`SourceVersion`	`character(1)` Version of original file.
`SourceLastModifiedDate`	`POSIXct()` The date when the source was last modified.
`SourceMd5`	`character()` md5 hash of original file.
`SourceSize`	`numeric(1)` Size of original file in bytes.
`DataProvider`	`character(1)` Provider of original data, e.g., NCBI, UniProt etc.
`Title`	`character(1)` Title for the resource with version or genome build as appropriate.
`Description`	`character(1)` Description of the resource. May include details such as data type, format, study origin, sequencing technology, treated vs control, number of samples etc.
`Species`	`character(1)` Species name. For help on valid species see `getSpeciesList, validSpecies, or suggestSpecies.`
`TaxonomyId`	`character(1)` NCBI code. There are checks for valid taxonomyId given the Species which produce warnings. See GenomeInfoDb::loadTaxonomyDb() for full validation table.
`Genome`	`character(1)` Name of genome build.
`Tags`	`character()` Free-form tags that serve as search terms.
`Recipe`	`character(1)` Name of recipe function. Only applicable to recipes created by the Bioconductor core team and included in AnnotationHubData base code.
`RDataClass`	`character()` Class of derived R object, e.g., GRanges. Length must match the length of `RDataPath`.
`RDataDateAdded`	`POSIXct()` Date resource was added to AnnotationHub. The default is today's date and is auto-generated when metadata are constructed. Resources will appear in snapshots with a date greater than or equal to the `RDataDateAdded`.
`RDataPath`	`character()` File path to where object is stored in AWS S3 bucket or on the web.This field should be the remainder of the path to the resource. The `Location_Prefix` will be prepended to `RDataPath` for the full path to the resource. If the resource is stored in Bioconductor's AWS S3 buckets, it should start with the name of the package associated with the metadata and should not start with a leading slash. It should include the resource file name. For strongly associated files, like a bam file and its index file, the two files should be separates with a colon `:`. This will link a single hub id with the multiple files.
`Maintainer`	`character(1)` Maintainer name and email address, ‘A Maintainer [email protected]’
`BiocVersion`	`character(1)`. The first Bioconductor version the resource was made available for. Unless removed from the hub, the resource will be available for all versions greater than or equal to this field.
`Coordinate_1_based`	`logical(1)` Do coordinates start with 1 or 0?
`DispatchClass`	`character(1)`. Determines how data are loaded into R. The value for this field should be ‘Rda’ if the data were serialized with `save()` and ‘Rds’ if serialized with `saveRDS`. The filename should have the appropriate ‘rda’ or ‘rds’ extension. A number of dispatch classes are pre-defined in AnnotationHub/R/AnnotationHubResource-class.R with the suffix ‘Resource’. For example, if you have sqlite files, the AnnotationHubResource-class.R defines SQLiteFileResource so the DispatchClass would be SQLiteFile. Contact [email protected] if you are not sure which class to use. The function `AnnotationHub::DispatchClassList()` will output a matrix of currently implemented DispatchClass and brief description of utility. If a predefine class does not seem appropriate contact [email protected].
`Location_Prefix`	`character(1)` URL location of AWS S3 bucket or web site where resource is located.
`Notes`	`character()` Notes about the resource.
`ahm`	An instance of class `AnnotationHubMetadata`.
`x`	An instance of class `AnnotationHubMetadata`.
`object`	An `AnnotationHubRecipe` instance.
`species`	`character(1)` The organism, e.g., "Homo sapiens".
`genome`	`character(1)` The genome build, e.g., "hg19".
`id`	An id whose DB record is to be fully deleted.
`objName`	`character(1)` The name of the PreparerClass used for dispatch.
`makeAnnotationHubMetadataFunction`	`function` Function (name) that makes `AnnotationHubMetadata` objects from the resource(s).
`where`	Environment where function definition is defined. Default value is sufficient.
`...`	Additional arguments passed to methods.

Value

AnnotationHubMetadata returns an instance of the class.

jsonPath returns a character(1)) representation of the full path to the location of the json file associated with this record.

toJson returns the JSON representation of the record.

fromJson retuns an instance of the class, as parsed from the JSON file.

Objects from the Class

Objects can be created by calls to the constructor, AnnotationHubMetadata().

Author(s)

Dan Tenenbaum and Marc Carlson

Examples

getClass("AnnotationHubMetadata")
getClass("AnnotationHubMetadata")

flog

Description

Write logging message to console and a file.

Usage

flog(level, ...)
flog(level, ...)

Arguments

`level`	A `characater(1)` string object.
`...`	Further arguments.

Details

Writes the message to the console and to a file.

Value

None.

Author(s)

Dan Tenenbaum

Class `ImportPreparer` and generic `newResources`

Description

The ImportPreparer and derived classes are used for dispatch during data discovery (see newResources). There is one ImportPreparer class for each data source for AnnotationHubMetadata.

newResources is a generic function; with methods implemented for each ImportPreparer.

Author(s)

Martin Morgan

Examples

getImportPreparerClasses()
getImportPreparerClasses()

Make AnnotationHubMetadata objects from csv file of metadata

Description

Make AnnotationHubMetadata objects from .csv files located in the "inst/extdata/" package directory of an AnnotationHub package.

Usage

  makeAnnotationHubMetadata(pathToPackage, fileName=character())
makeAnnotationHubMetadata(pathToPackage, fileName=character())

Arguments

`pathToPackage`	Full path to data package including the package name; no trailing slash
`fileName`	Name of metadata file(s) with csv extension. If none are provided, all files with .csv extension in "inst/extdata" will be processed.

Details

makeAnnotationHubMetadata: Reads the resource metadata from .csv files into a AnnotationHubMetadata object. The AnnotationHubMetadata is inserted in the AnnotationHub database. Intended for internal use or package authors checking the validity of package metadata.

Formatting metadata files:

makeAnnotationHubMetadata reads .csv files of metadata located in "inst/extdata". Internal functions perform checks for required columns and data types and can be used by package authors to validate their metadata before submitting the package for review.

The rows of the .csv file(s) represent individual Hub resources (i.e., data objects) and the columns are the metadata fields. All fields should be a single character string of length 1.

Required Fields in metadata file:
- Title: character(1). Name of the resource. This can be the exact file name (if self-describing) or a more complete description.
- Description: character(1). Brief description of the resource, similar to the 'Description' field in a package DESCRIPTION file.
- BiocVersion: character(1). The first Bioconductor version the resource was made available for. Unless removed from the hub, the resource will be available for all versions greater than or equal to this field. Generally the current devel version of Bioconductor.
- Genome: character(1). Genome. Can be NA.
- SourceType: character(1). Format of original data, e.g., FASTA, BAM, BigWig, etc. getValidSourceTypes() list currently acceptable values. If nothing seems appropiate for your data reach out to [email protected].
- SourceUrl: character(1). Optional location of original data files. Multiple urls should be provided as a comma separated string.
- SourceVersion: character(1). Version of original data.
- Species: character(1). Species. For help on valid species see getSpeciesList, validSpecies, or suggestSpecies. Can be NA.
- TaxonomyId: character(1). Taxonomy ID. There are checks for valid taxonomyId given the Species which produce warnings. See GenomeInfoDb::loadTaxonomyDb() for full validation table. Can be NA.
- Coordinate_1_based: logical. TRUE if data are 1-based. Can be NA
- DataProvider: character(1). Name of company or institution that supplied the original (raw) data.
- Maintainer: character(1). Maintainer name and email in the following format: Maintainer Name <username@address>.
- RDataClass: character(1). R / Bioconductor class the data are stored in, e.g., GRanges, SummarizedExperiment, ExpressionSet etc. If the file is loaded or read into R what is the class of the object.
- DispatchClass: character(1). Determines how data are loaded into R. The value for this field should be ‘Rda’ if the data were serialized with save() and ‘Rds’ if serialized with saveRDS. The filename should have the appropriate ‘rda’ or ‘rds’ extension. There are other available DispathClass types and the function AnnotationHub::DispatchClassList()
  
  A number of dispatch classes are pre-defined in AnnotationHub/R/AnnotationHubResource-class.R with the suffix ‘Resource’. For example, if you have sqlite files, the AnnotationHubResource-class.R defines SQLiteFileResource so the DispatchClass would be SQLiteFile. Contact [email protected] if you are not sure which class to use. The function AnnotationHub::DispatchClassList() will output a matrix of currently implemented DispatchClass and brief description of utility. If a predefine class does not seem appropriate contact [email protected]. An all purpose DispathClass is FilePath that instead of trying to load the file into R, will only return the path to the locally downloaded file.
- Location_Prefix: character(1). Do not include this field if data are stored in the Bioconductor AWS S3; it will be generated automatically.
  
  If data will be accessed from a location other than AWS S3 this field should be the base url.
- RDataPath: character().This field should be the remainder of the path to the resource. The Location_Prefix will be prepended to RDataPath for the full path to the resource. If the resource is stored in Bioconductor's AWS S3 buckets, it should start with the name of the package associated with the metadata and should not start with a leading slash. It should include the resource file name. For strongly associated files, like a bam file and its index file, the two files should be separates with a colon :. This will link a single hub id with the multiple files.
- Tags: character() vector. ‘Tags’ are search terms used to define a subset of resources in a Hub object, e.g, in a call to query.
  
  ‘Tags’ are automatically generated from the ‘biocViews’ in the DESCRIPTION and applied to all resources of the metadata file. Optionally, maintainers can define ‘Tags’ column of the metadata to define tags for each resource individually. Multiple ‘Tags’ are specified as a colon separated string, e.g., tags for two resources would look like this:
```
	     Tags=c("tag1:tag2:tag3", "tag1:tag3")
	     
```
NOTE: The metadata file can have additional columns beyond the 'Required Fields' listed above. These values are not added to the Hub database but they can be used in package functions to provide an additional level of metadata on the resources.

More on Location_Prefix and RDataPath. These two fields make up the complete file path url for downloading the data file. If using the Bioconductor AWS S3 bucket the Location_Prefix should not be included in the metadata file[s] as this field will be populated automatically. The RDataPath will be the directory structure you uploaded to S3. If you uploaded a directory ‘MyAnnotation/’, and that directory had a subdirectory ‘v1/’ that contained two files ‘counts.rds’ and ‘coldata.rds’, your metadata file will contain two rows and the RDataPaths would be ‘MyAnnotation/v1/counts.rds’ and ‘MyAnnotation/v1/coldata.rds’. If you host your data on a publicly accessible site you must include a base url as the Location_Prefix. If your data file was at ‘ftp://myinstiututeserver/biostats/project2/counts.rds’, your metadata file will have one row and the Location_Prefix would be ‘ftp://myinstiututeserver/’ and the RDataPath would be ‘biostats/project2/counts.rds’.

Value

A named list the length of fileName. Each element is a list of of AnnotationHubMetadata objects created from the .csv file.

Examples


## Each row of the metadata file represents a resource added to one of
## the 'Hubs'. This example creates a metadata.csv file for a single resource.
## In the case of multiple resources, the arguments below would be character
## vectors that produced multiple rows in the data.frame.

meta <- data.frame(
    Title = "RNA-Sequencing dataset from study XYZ",
    Description = paste0("RNA-seq data from study XYZ containing 10 normal ",
			 "and 10 tumor samples represented as a",
			 "SummarizedExperiment"),
    BiocVersion = "3.4",
    Genome = "GRCh38",
    SourceType = "BAM",
    SourceUrl = "http://www.path/to/original/data/file",
    SourceVersion = "Jan 01 2016",
    Species = "Homo sapiens",
    TaxonomyId = 9606,
    Coordinate_1_based = TRUE,
    DataProvider = "GEO",
    Maintainer = "Your Name <[email protected]>",
    RDataClass = "SummarizedExperiment",
    DispatchClass = "Rda",
    ResourceName = "FileName.rda"
)

## Not run: 
## Write the data out and put in the inst/extdata directory.
write.csv(meta, file="metadata.csv", row.names=FALSE)

## Test the validity of metadata.csv
makeAnnotationHubMetadata("path/to/mypackage")

## End(Not run)
## Each row of the metadata file represents a resource added to one of
## the 'Hubs'. This example creates a metadata.csv file for a single resource.
## In the case of multiple resources, the arguments below would be character
## vectors that produced multiple rows in the data.frame.

meta <- data.frame(
    Title = "RNA-Sequencing dataset from study XYZ",
    Description = paste0("RNA-seq data from study XYZ containing 10 normal ",
			 "and 10 tumor samples represented as a",
			 "SummarizedExperiment"),
    BiocVersion = "3.4",
    Genome = "GRCh38",
    SourceType = "BAM",
    SourceUrl = "http://www.path/to/original/data/file",
    SourceVersion = "Jan 01 2016",
    Species = "Homo sapiens",
    TaxonomyId = 9606,
    Coordinate_1_based = TRUE,
    DataProvider = "GEO",
    Maintainer = "Your Name <[email protected]>",
    RDataClass = "SummarizedExperiment",
    DispatchClass = "Rda",
    ResourceName = "FileName.rda"
)

## Not run: 
## Write the data out and put in the inst/extdata directory.
write.csv(meta, file="metadata.csv", row.names=FALSE)

## Test the validity of metadata.csv
makeAnnotationHubMetadata("path/to/mypackage")

## End(Not run)

Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.

Description

Transform an Ensembl FASTA file to a Bioconductor FaFile or ToBitFile.

Usage

makeEnsemblFastaToAHM(currentMetadata, baseUrl = "ftp://ftp.ensembl.org/pub/",
                      baseDir = "fasta/", release,
                      justRunUnitTest = FALSE,
                      BiocVersion = BiocManager::version())

makeEnsemblTwoBitToAHM(currentMetadata, baseUrl = "ftp://ftp.ensembl.org/pub/",
                       baseDir = "fasta/", release,
                       justRunUnitTest = FALSE,
                       BiocVersion = BiocManager::version())

ensemblFastaToFaFile(ahm)

ensemblFastaToTwoBitFile(ahm)
makeEnsemblFastaToAHM(currentMetadata, baseUrl = "ftp://ftp.ensembl.org/pub/",
                      baseDir = "fasta/", release,
                      justRunUnitTest = FALSE,
                      BiocVersion = BiocManager::version())

makeEnsemblTwoBitToAHM(currentMetadata, baseUrl = "ftp://ftp.ensembl.org/pub/",
                       baseDir = "fasta/", release,
                       justRunUnitTest = FALSE,
                       BiocVersion = BiocManager::version())

ensemblFastaToFaFile(ahm)

ensemblFastaToTwoBitFile(ahm)

Arguments

`currentMetadata`	Currently not used. Intended to be a list of metadata to filter, i.e., records that do not need to be processed again. Need to remove or fix.
`baseUrl`	ftp file location.
`baseDir`	ftp file directory.
`release`	Integer version number, e.g., "84".
`justRunUnitTest`	A `logical`. When TRUE, a small number of records (usually 5) are processed instead of all.
`BiocVersion`	A `character(1)` Bioconductor version. The resource will be available in Bioconductor >= to this version. Default value is the current version, specified with BiocManager::version().
`ahm`	List of `AnnotationHubMetadata` instances.

Details

makeEnsemblFastaToAHM and makeEnsemblTwoBitToAHM process metadata into a list of AnnotationHubMetadata objects.

ensemblFastaToFaFile unzips a .gz files, creates and index and writes out .rz and .rz.fai files to disk. ensemblFastaToTwoBit converts a fasta file to twobit format and writes the .2bit file out to disk.

Value

makeEnsemblFastaToAHM and makeEnsemblTwoBitToAHM return a list of AnnotationHubMetadata objects.

ensemblFastaToFaFile write out .rz and .rz.fai files to disk. ensemblFastaToTwoBit writes out a .2bit file to disk.

Author(s)

Bioconductor Core Team

Examples

## updateResources() generates metadata, process records and
## pushes files to AWS S3 buckets. See ?updateResources for details.

## 'release' is passed to makeEnsemblFastaToFaFile.
## Not run: 
meta <- updateResources("/local/path", 
                        BiocVersion = c("3.2", "3.3"),
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = FALSE, release = "83")

## End(Not run)
## updateResources() generates metadata, process records and
## pushes files to AWS S3 buckets. See ?updateResources for details.

## 'release' is passed to makeEnsemblFastaToFaFile.
## Not run: 
meta <- updateResources("/local/path", 
                        BiocVersion = c("3.2", "3.3"),
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = FALSE, release = "83")

## End(Not run)

Recipe to add Gencode FASTA resources to AnnotationHub

Description

Create metadata and process raw Gencode FASTA files for inclusion in AnnotationHub

Usage

makeGencodeFastaToAHM(currentMetadata, 
                      baseUrl="ftp://ftp.ebi.ac.uk/pub/databases/gencode/",
                      species=c("Human", "Mouse"), release, 
                      justRunUnitTest=FALSE, 
                      BiocVersion=BiocManager::version())

gencodeFastaToFaFile(ahm)
makeGencodeFastaToAHM(currentMetadata, 
                      baseUrl="ftp://ftp.ebi.ac.uk/pub/databases/gencode/",
                      species=c("Human", "Mouse"), release, 
                      justRunUnitTest=FALSE, 
                      BiocVersion=BiocManager::version())

gencodeFastaToFaFile(ahm)

Arguments

`currentMetadata`	Currently not used. Intended to be a list of metadata to filter, i.e., records that do not need to be processed again. Need to remove or fix.
`baseUrl`	ftp file location.
`species`	A `character(1)` of the species. Currently "Human" and "Mouse" are supported.
`release`	A `character` string of the release number.
`justRunUnitTest`	A `logical`. When TRUE, a small number of records (usually 5) are processed instead of all.
`BiocVersion`	A `character` vector of Bioconductor versions the resources should be available for.
`ahm`	List of `AnnotationHubMetadata` instances.

Details

Documentation:: http://www.gencodegenes.org/releases/
File download location:: ftp://ftp.ebi.ac.uk/pub/databases/gencode/. Gencode_human and Gencode_mouse are used.
Files downloaded:: Code is currently specific for human and mouse. Files chosen for download are described in AnnotationHubData:::.gencodeDescription().

Value

makeGencodeFastaAHM returns a list of AnnotationHubMetadata instances. gencodeFastaToFaFile returns nothing.

Author(s)

Bioconductor Core Team.

Examples


## updateResources() generates metadata, process records and
## pushes files to AWS S3 buckets. 

## To run the GencodeFasta recipe specify 
## 'preparerClasses = GencodeFastaImportPreparer'. The 'species' and 'release' 
## arguments are passed to makeGencodeFastaAHM().
## Not run: 
meta <- updateResources("/local/path", 
                        BiocVersion = c("3.2", "3.3"),
                        preparerClasses = "GencodeFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = FALSE)


## End(Not run)
## updateResources() generates metadata, process records and
## pushes files to AWS S3 buckets. 

## To run the GencodeFasta recipe specify 
## 'preparerClasses = GencodeFastaImportPreparer'. The 'species' and 'release' 
## arguments are passed to makeGencodeFastaAHM().
## Not run: 
meta <- updateResources("/local/path", 
                        BiocVersion = c("3.2", "3.3"),
                        preparerClasses = "GencodeFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = FALSE)


## End(Not run)

Functions to add OrgDb and TxDb sqlite files to AnnotationHub

Description

Add OrgDb and TxDb sqlite files to AnnotationHub

Usage

makeStandardOrgDbsToAHM(currentMetadata, justRunUnitTest = FALSE, 
                        BiocVersion = BiocManager::version(), 
                        downloadOrgDbs = TRUE)

makeStandardTxDbsToAHM(currentMetadata, justRunUnitTest = FALSE, 
                       BiocVersion = BiocManager::version(), TxDbs)

makeNCBIToOrgDbsToAHM(currentMetadata, justRunUnitTest = FALSE,
                      BiocVersion = BiocManager::version(), 
                      baseUrl = "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/")
makeStandardOrgDbsToAHM(currentMetadata, justRunUnitTest = FALSE, 
                        BiocVersion = BiocManager::version(), 
                        downloadOrgDbs = TRUE)

makeStandardTxDbsToAHM(currentMetadata, justRunUnitTest = FALSE, 
                       BiocVersion = BiocManager::version(), TxDbs)

makeNCBIToOrgDbsToAHM(currentMetadata, justRunUnitTest = FALSE,
                      BiocVersion = BiocManager::version(), 
                      baseUrl = "ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/")

Arguments

`currentMetadata`	Historically was intended to be a list of metadata to filter, i.e., records that do not need to be processed again. In some recipes this is used as a way to pass additional arguments. Need to remove or make consistent.
`baseUrl`	A `character()`. The file location.
`justRunUnitTest`	A `logical`. When TRUE, a small number of records (usually <= 5) are processed instead of all.
`BiocVersion`	A `character(1)`. The resource will be available for Bioconductor versions greater than and equal to this version. Default is BiocManaer::version().
`TxDbs`	Character vector of the `TxDb` names; generally includes `TxDbs` that were new or updated for the current release.
`downloadOrgDbs`	A `logical`. Indicates if all `OrgDb` packages in the Bioconductor repo should be downloaded and installed. This should be `TRUE` the first time the recipe is run and can be `FALSE` for subsequent runs when testing.

Details

makeStandardOrgDbsToAHM and makeStandardTxDbsToAHM extracts the sqlite files from the existing OrgDb and TxDb packages in the Bioconductor repositories and generate associated metadata.

makeNCBIToOrgDbsToAHM creates sqlite files and metadata for 1000 organisms with the makeOrgPackageFromNCBI function. These organisms are less 'main stream' than those hosted in the Bioconductor repository (makeStandardOrgDbsToAHM) and the databases are less comprehensive because data only come from one source, NCBI.

Value

List of AnnotationHubMetadata objects.

Author(s)

Bioconductor Core Team

Examples

## Not run: 
## In Bioconductor 3.5, one new TxDb was added and 4 active
## tracks were updated. This piece of code shows how to add these 5
## packages to AnnotationHub.

## Step I: generate metadata 
##
## Generate the metadata with the low-level helper for inspection.
TxDbs <- c("TxDb.Ggallus.UCSC.galGal5.refGene",
           "TxDb.Celegans.UCSC.ce11.refGene",
           "TxDb.Rnorvegicus.UCSC.rn5.refGene",
           "TxDb.Dmelanogaster.UCSC.dm6.ensGene",
           "TxDb.Rnorvegicus.UCSC.rn6.refGene")
meta <- makeStandardTxDbsToAHM(currentMetadata=list(AnnotationHubRoot="TxDbs"), 
                               justRunUnitTest=FALSE, 
                               TxDbs = TxDbs)

## Once the low-level helper runs with no errors, try generating the
## metadata with the high-level wrapper updateResources(). Setting
## metadataOnly=TRUE will generate metadata only and not push resources
## to data bucket. insert=FALSE prevents the metadata from being inserted in the
## database.
##
## The metadata generated by updateResources() will be the same as that
## generated by makeStandardTxDbsToAHM(). Both should be a list the same
## length as the number of TxDbs specified.
meta <- updateResources("TxDbs",
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=TRUE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)

INFO [2017-04-11 09:12:09] Preparer Class: TxDbFromPkgsImportPreparer
complete!
> length(meta)
[1] 5

## Step II: push resources to Azure 
##
## If the metadata looks correct we are ready to push resources to Azure.
## Set metadataOnly=FALSE but keep insert=FALSE.

## export an environment variable with a core generated SAS URL for
##   upload example:
##  export AZURE_SAS_URL='https://bioconductorhubs.blob.core.windows.net/staginghub?sp=racwl&st=2022-02-08T15:57:00Z&se=2022-02-22T23:57:00Z&spr=https&sv=2020-08-04&sr=c&sig=fBtPzgrw1Akzlz

meta <- updateResources("TxDbs",
                        BiocVersion="3.5",
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=FALSE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)

## Step III: insert metadata in AnnotationHub production database
##
## Inserting the metadata in the database is usually done as a separte step
## and with the help of the AnnotationHub docker.
## Set metadataOnly=TRUE and insert=TRUE.
meta <- updateResources("TxDbs",
                        BiocVersion="3.5",
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=FALSE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)


## End(Not run)
## Not run: 
## In Bioconductor 3.5, one new TxDb was added and 4 active
## tracks were updated. This piece of code shows how to add these 5
## packages to AnnotationHub.

## Step I: generate metadata 
##
## Generate the metadata with the low-level helper for inspection.
TxDbs <- c("TxDb.Ggallus.UCSC.galGal5.refGene",
           "TxDb.Celegans.UCSC.ce11.refGene",
           "TxDb.Rnorvegicus.UCSC.rn5.refGene",
           "TxDb.Dmelanogaster.UCSC.dm6.ensGene",
           "TxDb.Rnorvegicus.UCSC.rn6.refGene")
meta <- makeStandardTxDbsToAHM(currentMetadata=list(AnnotationHubRoot="TxDbs"), 
                               justRunUnitTest=FALSE, 
                               TxDbs = TxDbs)

## Once the low-level helper runs with no errors, try generating the
## metadata with the high-level wrapper updateResources(). Setting
## metadataOnly=TRUE will generate metadata only and not push resources
## to data bucket. insert=FALSE prevents the metadata from being inserted in the
## database.
##
## The metadata generated by updateResources() will be the same as that
## generated by makeStandardTxDbsToAHM(). Both should be a list the same
## length as the number of TxDbs specified.
meta <- updateResources("TxDbs",
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=TRUE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)

INFO [2017-04-11 09:12:09] Preparer Class: TxDbFromPkgsImportPreparer
complete!
> length(meta)
[1] 5

## Step II: push resources to Azure 
##
## If the metadata looks correct we are ready to push resources to Azure.
## Set metadataOnly=FALSE but keep insert=FALSE.

## export an environment variable with a core generated SAS URL for
##   upload example:
##  export AZURE_SAS_URL='https://bioconductorhubs.blob.core.windows.net/staginghub?sp=racwl&st=2022-02-08T15:57:00Z&se=2022-02-22T23:57:00Z&spr=https&sv=2020-08-04&sr=c&sig=fBtPzgrw1Akzlz

meta <- updateResources("TxDbs",
                        BiocVersion="3.5",
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=FALSE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)

## Step III: insert metadata in AnnotationHub production database
##
## Inserting the metadata in the database is usually done as a separte step
## and with the help of the AnnotationHub docker.
## Set metadataOnly=TRUE and insert=TRUE.
meta <- updateResources("TxDbs",
                        BiocVersion="3.5",
                        preparerClasses="TxDbFromPkgsImportPreparer",
                        metadataOnly=FALSE, insert = FALSE,
                        justRunUnitTest=FALSE, TxDbs = TxDbs)


## End(Not run)

updateResources

Description

Add new resources to AnnotationHub

Usage

updateResources(AnnotationHubRoot, BiocVersion = BiocManager::version(),
                preparerClasses = getImportPreparerClasses(),
                metadataOnly = TRUE, insert = FALSE,
                justRunUnitTest = FALSE, ...)

pushResources(allAhms, uploadToRemote = TRUE, download = TRUE)

pushMetadata(allAhms, url)
updateResources(AnnotationHubRoot, BiocVersion = BiocManager::version(),
                preparerClasses = getImportPreparerClasses(),
                metadataOnly = TRUE, insert = FALSE,
                justRunUnitTest = FALSE, ...)

pushResources(allAhms, uploadToRemote = TRUE, download = TRUE)

pushMetadata(allAhms, url)

Arguments

`AnnotationHubRoot`	Local path where files will be downloaded.
`BiocVersion`	A `character(1)` Bioconductor version. The resource will be available in Bioconductor >= to this version. Default value is the current version, specified with BiocManager::version().
`preparerClasses`	One of the `ImportPreparer` subclasses defined in `getImportPreparer()`. This class is used for dispatch during data discovery.
`metadataOnly`	A `logical` to specify the processing of metadata only or both metadata and data files. When FALSE, metadata are generated and data files are downloaded, processed and pushed to their final location in S3 buckets. `metadata = TRUE` produces only metadata and is useful for testing.
`insert`	NOTE: This option is for inserting metadata records in the production data base (done by Bioconductor core team member) and is for internal use only. A `logical` to control if metadata are inserted in the AnnotationHub db. By default this option is FALSE which is a useful state in which to test a new recipe and confirm the metadata fields are correct. When `insert = TRUE`, the "AH_SERVER_POST_URL" global option must be set to the http location of the AnnotationHubServer in the global environment or .Rprofile. Additionally, azcopy command line tools must be installed on the local machine to push files to Azure buckets. See upload_to_azure.
`justRunUnitTest`	A `logical`. When TRUE, a small number of records (usually 5) are processed instead of all.
`allAhms`	List of `AnnotationHubMetadata` objects.
`url`	URL of AnnotationHub database where metadata will be inserted.
`uploadToRemote`	A `logical` indicating whether resources should be uploaded to remote bioconductor default location. Currently Azure Data Lakes.
`download`	A `logical` indicating whether resources should be downloaded from resource url.
`...`	Arguments passed to other methods such as `regex`, `baseUrl`, `baseDir`.

Details

updateResources:

updateResources is responsible for creating metadata records and downloading, processing and pushing data files to their final resting place. The
preparerClasses argument is used in method dispatch to determine which recipe is used.

By manipulating the metadataOnly, insert and justRunUnitTest arguments one can flexibly test the metadata for a small number of records with or without downloading and processing the data files.
global options:

When insert = TRUE the "AH_SERVER_POST_URL" option must be set to the https location of the AnnotationHub db.

Value

A list of AnnotationHubMetadata objects.

Author(s)

Martin Morgan, Marc Carlson

Examples


## Not run: 

## -----------------------------------------------------------------------
## Inspect metadata:
## -----------------------------------------------------------------------
## A useful first step in testing a new recipe is to generate and
## inspect a small number of metadata records. The combination of
## 'metadataOnly=TRUE', 'insert=FALSE' and 'justRunUnitTest=TRUE'
## generates metadata for the first 5 records and does not download or
## process any data.

meta <- updateResources("/local/path",
                        BiocVersion = "3.3",
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = TRUE,
                        release = "84")

INFO [2015-11-12 07:58:05] Preparer Class: EnsemblFastaImportPreparer
Ailuropoda_melanoleuca.ailMel1.cdna.all.fa.gz
Ailuropoda_melanoleuca.ailMel1.dna_rm.toplevel.fa.gz
Ailuropoda_melanoleuca.ailMel1.dna_sm.toplevel.fa.gz
Ailuropoda_melanoleuca.ailMel1.dna.toplevel.fa.gz
Ailuropoda_melanoleuca.ailMel1.ncrna.fa.gz

## The return value is a list of metadata for the first 5 records:

> names(meta)
[1] "FASTA cDNA sequence for Ailuropoda melanoleuca"
[2] "FASTA DNA sequence for Ailuropoda melanoleuca"
[3] "FASTA DNA sequence for Ailuropoda melanoleuca"
[4] "FASTA DNA sequence for Ailuropoda melanoleuca"
[5] "FASTA ncRNA sequence for Ailuropoda melanoleuca"


## Each record is of class AnnotationHubMetadata:

> class(meta[[1]])
[1] "AnnotationHubMetadata"
attr(,"package")
[1] "AnnotationHubData"

## -----------------------------------------------------------------------
## Insert metadata in the db and process/push data files:
## -----------------------------------------------------------------------
## This next code chunk creates the metadata and downloads and processes
## the data (metadataOnly=FALSE). If all files are successfully pushed to
## to their final resting place, metadata records are inserted in the 
## AnnotationHub db (insert=TRUE). Metadata insertion is done by a 
## Bioconductor team member; contact [email protected] for help.

meta <- updateResources("local/path",
                        BiocVersion = "3.5",
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = FALSE, insert = TRUE,
                        justRunUnitTest = FALSE,
                        regex = ".*release-81")

## -----------------------------------------------------------------------
## Recovery helpers:
## -----------------------------------------------------------------------

## pushResources() and pushMetadata() are both called from updateResources()
## but can be used solo for testing or completing a run that
## terminated unexpectedly.

## Download, process and push to azure the last 2 files in 'meta':
sub <- meta[length(meta) - 1:length(meta)]
pushResources(sub)

## Insert metadata in the AnotationHub db for the last 2 files in 'meta':

pushMetadata(sub, url = getOption("AH_SERVER_POST_URL"))

## End(Not run)

## Not run: 

## -----------------------------------------------------------------------
## Inspect metadata:
## -----------------------------------------------------------------------
## A useful first step in testing a new recipe is to generate and
## inspect a small number of metadata records. The combination of
## 'metadataOnly=TRUE', 'insert=FALSE' and 'justRunUnitTest=TRUE'
## generates metadata for the first 5 records and does not download or
## process any data.

meta <- updateResources("/local/path",
                        BiocVersion = "3.3",
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = TRUE, insert = FALSE,
                        justRunUnitTest = TRUE,
                        release = "84")

INFO [2015-11-12 07:58:05] Preparer Class: EnsemblFastaImportPreparer
Ailuropoda_melanoleuca.ailMel1.cdna.all.fa.gz
Ailuropoda_melanoleuca.ailMel1.dna_rm.toplevel.fa.gz
Ailuropoda_melanoleuca.ailMel1.dna_sm.toplevel.fa.gz
Ailuropoda_melanoleuca.ailMel1.dna.toplevel.fa.gz
Ailuropoda_melanoleuca.ailMel1.ncrna.fa.gz

## The return value is a list of metadata for the first 5 records:

> names(meta)
[1] "FASTA cDNA sequence for Ailuropoda melanoleuca"
[2] "FASTA DNA sequence for Ailuropoda melanoleuca"
[3] "FASTA DNA sequence for Ailuropoda melanoleuca"
[4] "FASTA DNA sequence for Ailuropoda melanoleuca"
[5] "FASTA ncRNA sequence for Ailuropoda melanoleuca"


## Each record is of class AnnotationHubMetadata:

> class(meta[[1]])
[1] "AnnotationHubMetadata"
attr(,"package")
[1] "AnnotationHubData"

## -----------------------------------------------------------------------
## Insert metadata in the db and process/push data files:
## -----------------------------------------------------------------------
## This next code chunk creates the metadata and downloads and processes
## the data (metadataOnly=FALSE). If all files are successfully pushed to
## to their final resting place, metadata records are inserted in the 
## AnnotationHub db (insert=TRUE). Metadata insertion is done by a 
## Bioconductor team member; contact [email protected] for help.

meta <- updateResources("local/path",
                        BiocVersion = "3.5",
                        preparerClasses = "EnsemblFastaImportPreparer",
                        metadataOnly = FALSE, insert = TRUE,
                        justRunUnitTest = FALSE,
                        regex = ".*release-81")

## -----------------------------------------------------------------------
## Recovery helpers:
## -----------------------------------------------------------------------

## pushResources() and pushMetadata() are both called from updateResources()
## but can be used solo for testing or completing a run that
## terminated unexpectedly.

## Download, process and push to azure the last 2 files in 'meta':
sub <- meta[length(meta) - 1:length(meta)]
pushResources(sub)

## Insert metadata in the AnotationHub db for the last 2 files in 'meta':

pushMetadata(sub, url = getOption("AH_SERVER_POST_URL"))

## End(Not run)

Upload a file to Microsoft Azure Data Lake

Description

This function is for uploading a file resource to the Microsoft Azure Data Lake.

Usage

upload_to_azure(file, sas)upload_to_azure(file, sas)

Arguments

`file`	The file or directory to upload.
`sas`	A SAS url for the designated destination on Microsoft Azure Data Lake.

Details

Uses the azcopy Command Line Interface to copy a file to Microsoft Azure Data Lake. Assumes azcopy is properly installed and that the azcopy program is in your PATH. The function performs a recursive automatically so it can take a file or directory for upload. The SAS URL is generated on Azure by someone who has permission to the desired destination. Please be sure to use the SAS url and not the SAS token. The sas url can be provided as an argument; if the argument is not provided it will search for a system environment variable 'AZURE_SAS_URL'.

Value

TRUE on success. If the command fails, the function will exit with an error.

Author(s)

Lori Shepherd

Examples

## Not run: 
upload_to_azure("myfile.txt", "https://sasurl")

## End(Not run)
## Not run: 
upload_to_azure("myfile.txt", "https://sasurl")

## End(Not run)

Upload a file to Amazon S3

Description

This function is for uploading a file resource to the S3 cloud.

Usage

upload_to_S3(file, remotename, bucket, profile, acl="public-read")
upload_to_S3(file, remotename, bucket, profile, acl="public-read")

Arguments

`file`	The file to upload.
`remotename`	The name this file should have in S3, including any "keys" that are part of the name. This should not start with a slash (if it does, the leading slash will be removed), but can contain forward slashes.
`bucket`	Name of the S3 bucket to copy to.
`profile`	Corresponds to a profile set in the config file for the AWS CLI (see the documentation). If this argument is omitted,the default profile is used.
`acl`	Should be one of `private`, `public-read`, or `public-read-write`.

Details

Uses the AWS Command Line Interface to copy a file to Amazon S3. Assumes the CLI is properly configured and that the aws program is in your PATH. The CLI should be configured with the credentials of a user who has permission to upload to the appropriate bucket. It's recommended to use IAM to set up users with limited permissions.

There is an RAmazonS3 package but it seems to have issues uploading files to S3.

Value

TRUE on success. If the command fails, the function will exit with an error.

Author(s)

Dan Tenenbaum

Examples

## Not run: 
upload_to_S3("myfile.txt", "foo/bar/baz/yourfile.txt")
# If this is successful, the file should be accessible at 
# http://s3.amazonaws.com/annotationhub/foo/bar/baz/yourfile.txt

## End(Not run)
## Not run: 
upload_to_S3("myfile.txt", "foo/bar/baz/yourfile.txt")
# If this is successful, the file should be accessible at 
# http://s3.amazonaws.com/annotationhub/foo/bar/baz/yourfile.txt

## End(Not run)

ValidationFunctions

Description

Functions to assist in the validation process of creating the metadata.csv file for Hub Resources

Usage

getSpeciesList(verbose=FALSE)

validSpecies(species, verbose=TRUE)

suggestSpecies(query, verbose=FALSE, op=c("|", "&"))

getValidSourceTypes()

checkSpeciesTaxId(txid, species, verbose=TRUE)

validDispatchClass(dc, verbose=TRUE)
getSpeciesList(verbose=FALSE)

validSpecies(species, verbose=TRUE)

suggestSpecies(query, verbose=FALSE, op=c("|", "&"))

getValidSourceTypes()

checkSpeciesTaxId(txid, species, verbose=TRUE)

validDispatchClass(dc, verbose=TRUE)

Arguments

`species`	species to validate (may be single value or list)
`query`	terms to query. Whether AND or OR is determined by argument op.
`verbose`	should additional information and useful tips be displayed
`op`	Should searching of mulitple terms be conditional OR ("\|") or AND ("&")
`txid`	taxonomy id (single value or list)
`dc`	Dispatch class to validate (may be single value or list)

Details

getSpeciesList: Provides a list of valid species as determined by the GenomeInfoDbData package specData.rda file.
validSpecies: True/False if argument is considered a valid species based on the list generated by getSpeciesList. A species may be deemed invalid if the capitalization mismatches or punctuation mismatches. Use suggestSpecies to find similar terms.
suggestSpecies: Based on a term or multiple terms suggest possible valid species.
getValidSourceTypes: returns list of acceptable values for SourceType in metadata.csv. If you think a valid source type should be added to the list please reach out to [email protected]
checkSpeciesTaxId: cross validates a list of species and taxonomy ids for expected values based on GenomeInfoDb::loadTaxonomyDb(). Warning when there is a mismatch.
validDispatchClass: TRUE/FALSE if argument is considered a valid DispatchClass based on the currently available methods in AnnotationHub. Use AnnotationHub::DispatchClassList() to see the table of currently available methods. If a currently available method is not appropriate for your resource, please reach out to Lori Shepherd [email protected] to request a new method be added.

Value

For getSpeciesList: character vector of valid species
For validSpecies: True/False if all species given as argument are valid
For suggestSpecies: data.frame of taxonomy id and species name of possible valid species based on given query key words.
For getValidSourceTypes: character vector of valid source types.
For checkSpeciesTaxId: NULL if check is verfified, If verbose is ture a table of suggested values along with the warning.
For validDispatchClass: True/False if all dispatch class given as argument are valid

Author(s)

Lori Shepherd

Examples


species = getSpeciesList()

# following is TRUE

validSpecies("Homo sapiens")
# followin is FALSE because of starting "h"
validSpecies("homo sapiens")

# can provide multiple, if any are not valid FALSE
# TRUE
validSpecies(c("Homo sapiens", "Canis domesticus"))

suggestSpecies("Canis")

getValidSourceTypes()

checkSpeciesTaxId(1003232, "Edhazardia aedis")
checkSpeciesTaxId(9606, "Homo sapiens")

validDispatchClass("GRanges")
species = getSpeciesList()

# following is TRUE

validSpecies("Homo sapiens")
# followin is FALSE because of starting "h"
validSpecies("homo sapiens")

# can provide multiple, if any are not valid FALSE
# TRUE
validSpecies(c("Homo sapiens", "Canis domesticus"))

suggestSpecies("Canis")

getValidSourceTypes()

checkSpeciesTaxId(1003232, "Edhazardia aedis")
checkSpeciesTaxId(9606, "Homo sapiens")

validDispatchClass("GRanges")

Package 'AnnotationHubData'

Help Index

Transform public data resources into Bioconductor Data Structures

Description

Details

Author(s)

See Also

Class "AnnotationHubMetadata" and methods

Description

Usage

Arguments

Value

Objects from the Class

Author(s)

Examples

flog

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Class ImportPreparer and generic newResources

Description

Author(s)

See Also

Examples

Make AnnotationHubMetadata objects from csv file of metadata

Description

Usage

Arguments

Details

Value

See Also

Examples

Functions to convert Ensembl FASTA files to FaFile and TwoBitFile for inclusion in AnnotationHub.

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Recipe to add Gencode FASTA resources to AnnotationHub

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Functions to add OrgDb and TxDb sqlite files to AnnotationHub

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

updateResources

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Upload a file to Microsoft Azure Data Lake

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Class `"AnnotationHubMetadata"` and methods

Class `ImportPreparer` and generic `newResources`