1. SRAdb
  2. R
  3. getSRAdbFile.R
Browse code

update the download URL in SRAmetadb.sqlite.gz and bump the version

Zhu authored on 29/08/2022 20:32:24
Showing 1 changed files
R/getSRAdbFile.R
History View file @ 9f08c4c
... ... 
@@ -8,7 +8,7 @@ getSRAdbFile <-
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     localfile <- file.path(destdir, destfile)
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     options(warn=-1)
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-    url_sra_1 = 'https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz'
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+    url_sra_1 = 'https://gbnci.cancer.gov/backup/SRAmetadb.sqlite.gz'
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     url_sra_2 = 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
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     if(! inherits(try(url(url_sra_1, open='rb'), silent = TRUE), "try-error") ) {
Browse code

Updated download URLs in getSRAdbFile

zhujack authored on 28/09/2017 18:08:22
Showing 1 changed files
R/getSRAdbFile.R
History View file @ 278414c
... ... 
@@ -8,17 +8,13 @@ getSRAdbFile <-
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     localfile <- file.path(destdir, destfile)
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     options(warn=-1)
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-    url_sra_1 = 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
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-    url_sra_2 = 'https://dl.dropboxusercontent.com/u/51653511/SRAmetadb.sqlite.gz'
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-    url_sra_3 = 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz'
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-
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+    url_sra_1 = 'https://s3.amazonaws.com/starbuck1/sradb/SRAmetadb.sqlite.gz'
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+    url_sra_2 = 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
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     if(! inherits(try(url(url_sra_1, open='rb'), silent = TRUE), "try-error") ) {
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        url_sra = url_sra_1
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-    } else if(! inherits(try(url(url_sra_2, open='rb'), silent = TRUE), "try-error") ) {
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-       url_sra = url_sra_2
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     } else {
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-       url_sra = url_sra_3
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+       url_sra = url_sra_2
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     }
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     download.file(url_sra, destfile = localfile, mode = "wb", method=method)
Browse code

Update download link to https://gbnci-abcc.ncifcrf.gov

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SRAdb@117936 bc3139a8-67e5-0310-9ffc-ced21a209358

Jack Zhu authored on 27/05/2016 19:50:49
Showing 1 changed files
R/getSRAdbFile.R
History View file @ 4ad4faf
... ... 
@@ -8,9 +8,10 @@ getSRAdbFile <-
8 8 
     localfile <- file.path(destdir, destfile)
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     options(warn=-1)
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-    url_sra_1 = 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
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-    url_sra_2 = 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz'
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-    url_sra_3 = 'https://dl.dropboxusercontent.com/u/51653511/SRAmetadb.sqlite.gz'
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+    url_sra_1 = 'https://gbnci-abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
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+    url_sra_2 = 'https://dl.dropboxusercontent.com/u/51653511/SRAmetadb.sqlite.gz'
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+    url_sra_3 = 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz'
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+
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     if(! inherits(try(url(url_sra_1, open='rb'), silent = TRUE), "try-error") ) {
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        url_sra = url_sra_1
Browse code

Update the dropbox link to https://dl.dropboxusercontent.com/u/51653511/SRAmetadb.sqlite.gz and bump the version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SRAdb@116875 bc3139a8-67e5-0310-9ffc-ced21a209358

Jack Zhu authored on 28/04/2016 14:31:12
Showing 1 changed files
R/getSRAdbFile.R
History View file @ e4044f2
... ... 
@@ -10,7 +10,7 @@ getSRAdbFile <-
10 10
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     url_sra_1 = 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
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     url_sra_2 = 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz'
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-    url_sra_3 = 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz'
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+    url_sra_3 = 'https://dl.dropboxusercontent.com/u/51653511/SRAmetadb.sqlite.gz'
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     if(! inherits(try(url(url_sra_1, open='rb'), silent = TRUE), "try-error") ) {
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        url_sra = url_sra_1
Browse code

Added Dropbox URL as an alternative downloading source

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SRAdb@61005 bc3139a8-67e5-0310-9ffc-ced21a209358

Jack Zhu authored on 01/12/2011 03:14:49
Showing 1 changed files
R/getSRAdbFile.R
History View file @ bb8175a
... ... 
@@ -5,15 +5,22 @@ getSRAdbFile <-
5 5 
     if (missing(method))
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         method <- ifelse(!is.null(getOption("download.file.method")),
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                          getOption("download.file.method"), "auto")
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-    localfile <- file.path(destdir, destfile)
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-
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+    localfile <- file.path(destdir, destfile)
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     options(warn=-1)
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-    url_sra = "http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz"
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-    con.url_sra <- try(url(url_sra, open='rb'), silent = TRUE)
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-    if(inherits(con.url_sra, "try-error"))
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-    	url_sra = "http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz"
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+
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+    url_sra_1 = 'http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz'
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+    url_sra_2 = 'http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz'
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+    url_sra_3 = 'http://dl.dropbox.com/u/51653511/SRAmetadb.sqlite.gz'
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+
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+    if(! inherits(try(url(url_sra_1, open='rb'), silent = TRUE), "try-error") ) {
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+       url_sra = url_sra_1
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+    } else if(! inherits(try(url(url_sra_2, open='rb'), silent = TRUE), "try-error") ) {
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+       url_sra = url_sra_2
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+    } else {
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+       url_sra = url_sra_3
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+    }
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+
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     download.file(url_sra, destfile = localfile, mode = "wb", method=method)
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-
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     message("Unzipping...\n")
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     gunzip(localfile, overwrite = TRUE)
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     unzippedlocalfile <- gsub("[.]gz$", "", localfile)
Browse code

Added switch for downlaoding SRAmetadb.sqlite.gz from our alternativre server

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SRAdb@46096 bc3139a8-67e5-0310-9ffc-ced21a209358

Jack Zhu authored on 16/04/2010 14:55:14
Showing 1 changed files
R/getSRAdbFile.R
History View file @ 94d3134
... ... 
@@ -6,10 +6,14 @@ getSRAdbFile <-
6 6 
         method <- ifelse(!is.null(getOption("download.file.method")),
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                          getOption("download.file.method"), "auto")
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     localfile <- file.path(destdir, destfile)
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-    # download.file("http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz",
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-    #              destfile = localfile, mode = "wb", method=method)
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-	download.file("http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz",
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-				  destfile = localfile, mode = "wb", method=method)
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+
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+    options(warn=-1)
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+    url_sra = "http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz"
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+    con.url_sra <- try(url(url_sra, open='rb'), silent = TRUE)
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+    if(inherits(con.url_sra, "try-error"))
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+    	url_sra = "http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz"
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+    download.file(url_sra, destfile = localfile, mode = "wb", method=method)
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+
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     message("Unzipping...\n")
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     gunzip(localfile, overwrite = TRUE)
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     unzippedlocalfile <- gsub("[.]gz$", "", localfile)
Browse code

getSRAdbFile - download sqlite database from: http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SRAdb@46085 bc3139a8-67e5-0310-9ffc-ced21a209358

Jack Zhu authored on 16/04/2010 01:33:25
Showing 1 changed files
R/getSRAdbFile.R
History View file @ 3357184
... ... 
@@ -6,8 +6,10 @@ getSRAdbFile <-
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         method <- ifelse(!is.null(getOption("download.file.method")),
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                          getOption("download.file.method"), "auto")
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     localfile <- file.path(destdir, destfile)
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-    download.file("http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz",
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-                  destfile = localfile, mode = "wb", method=method)
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+    # download.file("http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz",
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+    #              destfile = localfile, mode = "wb", method=method)
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+	download.file("http://gbnci.abcc.ncifcrf.gov/backup/SRAmetadb.sqlite.gz",
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+				  destfile = localfile, mode = "wb", method=method)
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     message("Unzipping...\n")
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     gunzip(localfile, overwrite = TRUE)
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     unzippedlocalfile <- gsub("[.]gz$", "", localfile)
Browse code

Add SRAdb to SVN repository.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SRAdb@45876 bc3139a8-67e5-0310-9ffc-ced21a209358

Chao-Jen Wong authored on 12/04/2010 17:15:21
Showing 1 changed files
R/getSRAdbFile.R
History View file @ 5de8aa1
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,20 @@
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+getSRAdbFile <-
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+    function (destdir = getwd(), destfile = "SRAmetadb.sqlite.gz",
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+              method)
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+{
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+    if (missing(method))
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+        method <- ifelse(!is.null(getOption("download.file.method")),
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+                         getOption("download.file.method"), "auto")
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+    localfile <- file.path(destdir, destfile)
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+    download.file("http://watson.nci.nih.gov/~zhujack/SRAmetadb.sqlite.gz",
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+                  destfile = localfile, mode = "wb", method=method)
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+    message("Unzipping...\n")
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+    gunzip(localfile, overwrite = TRUE)
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+    unzippedlocalfile <- gsub("[.]gz$", "", localfile)
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+    con <- dbConnect(SQLite(), unzippedlocalfile)
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+    dat <- dbGetQuery(con, "SELECT * FROM metaInfo")
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+    dbDisconnect(con)
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+    message("Metadata associate with downloaded file:\n")
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+    message(dat)
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+    return(unzippedlocalfile)
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+}