A character vector of Bioconductor versions the resources should be
available for.
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
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.
...
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 = c("3.2", "3.3"),
preparerClasses = "EnsemblFastaImportPreparer",
metadataOnly = TRUE, insert = FALSE,
justRunUnitTest = TRUE,
regex = ".*release-82")
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. If all files are successfully pushed to their
## final resting place then metadata are inserted in the AnnotationHub db.
meta <- updateResources("local/path",
BiocVersion = c("3.2", "3.3"),
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)