updateResources: updateResources

In AnnotationHubData: Transform public data resources into Bioconductor Data Structures

Description

Add new resources to AnnotationHub

Usage

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

pushResources(allAhms, uploadToS3 = 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, AWS command line tools must be installed on the local machine to push files to S3 buckets. See https://aws.amazon.com/cli/ for installation instructions.
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.
uploadToS3	A logical indicating whether resources should be uploaded to the AWS S3 bucket.
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:

  Several recipes look at the "AnnotationHub_Use_Disk" option to determine if the file is written to S3. This is legacy behavior and not clearly documented. If the recipe being run respects this option it must be set before running updateResources,

  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

See Also

• AnnotationHubMetadata

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 [e-mail] 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 S3 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)

AnnotationHubData documentation built on April 17, 2021, 6:05 p.m.