## 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)
Run the code above in your browser using DataCamp Workspace