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fix local processing

Simone authored on 25/04/2021 14:30:39
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@@ -35,8 +35,9 @@ execute <- function() {
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   WrappeR <- J("it/polimi/genomics/r/Wrapper")
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   remote_proc <- WrappeR$is_remote_processing()
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   datasets <- .jevalArray(WrappeR$get_dataset_list(), simplify = TRUE)
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+  exists_credential <- exists("GMQL_credentials", envir = .GlobalEnv)
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-  if(!remote_proc)
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+  if(!remote_proc && exists_credential)
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     .download_or_upload(datasets)
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   response <- WrappeR$execute()
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@@ -30,7 +30,11 @@ corresponding prefix.}
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 \item{region_attributes}{vector of strings that extracts only region
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 attributes  specified; if NULL no regions attribute is taken and the output
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 is only GRanges made up by the region coordinate attributes
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-(seqnames, start, end, strand)}
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+(seqnames, start, end, strand);
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+It is also possible to assign the \code{\link{FULL}} with or without 
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+its input parameter; in case was without the `except` parameter, 
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+all the region attributes are taken, otherwise all the region attributes 
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+are taken except the input attribute defined by except.}
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 \item{suffix}{name for each metadata column of GRanges. By default it is the
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 value of the metadata attribute named "antibody_target". This string is
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@@ -75,19 +79,14 @@ grl <- import_gmql(test_path, TRUE)
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 sorted_grl <- sort(grl)
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 filter_and_extract(sorted_grl, region_attributes = c("pvalue", "peak"))
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-## It is also possible to define the region attributes, using the FULL() 
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-## function parameter, in order to includes every region 
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-## attributes present into the schema file
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+## This statement imports a GMQL dataset as GRangesList and filters it
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+## including all the region attributes
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 sorted_grl_full <- sort(grl)
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-filter_and_extract(sorted_grl, region_attributes = FULL())
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+filter_and_extract(sorted_grl_full, region_attributes = FULL())
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-grl <- import_gmql(test_path, TRUE)
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-sorted_grl <- sort(grl)
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-filter_and_extract(sorted_grl, region_attributes = FULL())
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-
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-## Also, we can inlcude a list of region attribute inside the FULL() 
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-## function to exlucde that regions
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+## This statement imports a GMQL dataset as GRangesList and filters it
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+## including all the region attributes except "jaccard" and "score"
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 sorted_grl_full_except <- sort(grl)
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 filter_and_extract(