From 47833bb5e25153fa61d29fcd677df4999841218e Mon Sep 17 00:00:00 2001 From: Marcin Pilarczyk Date: Mon, 11 Nov 2019 16:21:14 -0800 Subject: [PATCH 1/4] Added time stamped to files to upload --- usingIlincsApis.Rmd | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/usingIlincsApis.Rmd b/usingIlincsApis.Rmd index 56aec94..183aa4e 100644 --- a/usingIlincsApis.Rmd +++ b/usingIlincsApis.Rmd @@ -176,15 +176,17 @@ head(sigs,n=10) ## Find connected signatures based on user submitted full signature ##### Creating a file to upload from previouslsy downloaded signature file ```{r} -write.table(signatureData,file="sigFile.tsv",sep="\t",row.names=F,col.names = T,quote=F) -system(paste("head sigFile.tsv")) +timeStamp <- format(Sys.time(), "%Y_%b_%d_%H_%M_%S") +tsvFileName <- paste("sigFile",timeStamp,".tsv",sep="") +write.table(signatureData,file=tsvFileName,sep="\t",row.names=F,col.names = T,quote=F) +system(paste("head ",tsvFileName,sep="")) ``` ### Upload the file ```{r connected signatures by uploading signature file} apiUrl<-"http://www.ilincs.org/api/SignatureMeta/upload" -sigFile <- "sigFile.tsv" -req <- POST(apiUrl, body=list(file=upload_file("sigFile.tsv"))) +sigFile <- tsvFileName +req <- POST(apiUrl, body=list(file=upload_file(tsvFileName))) signatureFile <- httr::content(req)$status$fileName[[1]] signatureFile ``` From 83b9b745c25c0334a299375b2562f3009097080d Mon Sep 17 00:00:00 2001 From: Marcin Pilarczyk Date: Tue, 12 Nov 2019 15:19:44 -0800 Subject: [PATCH 2/4] Used unique subfolders for upload Needs to be cleaned --- usingIlincsApis.Rmd | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/usingIlincsApis.Rmd b/usingIlincsApis.Rmd index 183aa4e..80b040a 100644 --- a/usingIlincsApis.Rmd +++ b/usingIlincsApis.Rmd @@ -176,18 +176,31 @@ head(sigs,n=10) ## Find connected signatures based on user submitted full signature ##### Creating a file to upload from previouslsy downloaded signature file ```{r} -timeStamp <- format(Sys.time(), "%Y_%b_%d_%H_%M_%S") -tsvFileName <- paste("sigFile",timeStamp,".tsv",sep="") +# timeStamp <- format(Sys.time(), "%Y_%b_%d_%H_%M_%S") +# tsvFileName <- paste("sigFile",timeStamp,".tsv",sep="") +tsvFileName <- "sigFile.tsv" write.table(signatureData,file=tsvFileName,sep="\t",row.names=F,col.names = T,quote=F) system(paste("head ",tsvFileName,sep="")) ``` ### Upload the file ```{r connected signatures by uploading signature file} -apiUrl<-"http://www.ilincs.org/api/SignatureMeta/upload" +# apiUrl<-"http://www.ilincs.org/api/SignatureMeta/upload" +apiUrl<-"http://www.ilincs.org/api/SignatureUploads/uploadToiLINCS" sigFile <- tsvFileName req <- POST(apiUrl, body=list(file=upload_file(tsvFileName))) -signatureFile <- httr::content(req)$status$fileName[[1]] +# signatureFile <- httr::content(req)$status$fileName[[1]] +# signatureFile +# res <- httr::content(req) +# res +uploadID <- httr::content(req)$id +uploadID +apiUrl <- paste("http://www.ilincs.org/api/ilincsR/uploadSignature") +# req <- GET(apiUrl) +req <- POST(apiUrl, body=list(file=tsvFileName,path=uploadID), encode = "form") +# res <- httr::content(req) +# res +signatureFile <- httr::content(req)$fileName[[1]] signatureFile ``` ### Find connected signatures From 73ff40b4cdbb1d2df3d04db3ee5c4db4a5d2b58a Mon Sep 17 00:00:00 2001 From: Marcin Pilarczyk Date: Tue, 12 Nov 2019 15:22:14 -0800 Subject: [PATCH 3/4] Cleaned up upload code --- usingIlincsApis.Rmd | 10 ---------- 1 file changed, 10 deletions(-) diff --git a/usingIlincsApis.Rmd b/usingIlincsApis.Rmd index 80b040a..03aa757 100644 --- a/usingIlincsApis.Rmd +++ b/usingIlincsApis.Rmd @@ -176,8 +176,6 @@ head(sigs,n=10) ## Find connected signatures based on user submitted full signature ##### Creating a file to upload from previouslsy downloaded signature file ```{r} -# timeStamp <- format(Sys.time(), "%Y_%b_%d_%H_%M_%S") -# tsvFileName <- paste("sigFile",timeStamp,".tsv",sep="") tsvFileName <- "sigFile.tsv" write.table(signatureData,file=tsvFileName,sep="\t",row.names=F,col.names = T,quote=F) system(paste("head ",tsvFileName,sep="")) @@ -185,21 +183,13 @@ system(paste("head ",tsvFileName,sep="")) ### Upload the file ```{r connected signatures by uploading signature file} -# apiUrl<-"http://www.ilincs.org/api/SignatureMeta/upload" apiUrl<-"http://www.ilincs.org/api/SignatureUploads/uploadToiLINCS" sigFile <- tsvFileName req <- POST(apiUrl, body=list(file=upload_file(tsvFileName))) -# signatureFile <- httr::content(req)$status$fileName[[1]] -# signatureFile -# res <- httr::content(req) -# res uploadID <- httr::content(req)$id uploadID apiUrl <- paste("http://www.ilincs.org/api/ilincsR/uploadSignature") -# req <- GET(apiUrl) req <- POST(apiUrl, body=list(file=tsvFileName,path=uploadID), encode = "form") -# res <- httr::content(req) -# res signatureFile <- httr::content(req)$fileName[[1]] signatureFile ``` From 743b3781a230ae590a7e74d79ea3b809e14cefdd Mon Sep 17 00:00:00 2001 From: Marcin Pilarczyk Date: Tue, 12 Nov 2019 15:35:31 -0800 Subject: [PATCH 4/4] removed line that is not needed --- usingIlincsApis.Rmd | 1 - 1 file changed, 1 deletion(-) diff --git a/usingIlincsApis.Rmd b/usingIlincsApis.Rmd index 03aa757..37edaf5 100644 --- a/usingIlincsApis.Rmd +++ b/usingIlincsApis.Rmd @@ -184,7 +184,6 @@ system(paste("head ",tsvFileName,sep="")) ### Upload the file ```{r connected signatures by uploading signature file} apiUrl<-"http://www.ilincs.org/api/SignatureUploads/uploadToiLINCS" -sigFile <- tsvFileName req <- POST(apiUrl, body=list(file=upload_file(tsvFileName))) uploadID <- httr::content(req)$id uploadID