From 113e82d34b97fea6fa39c68171b356ad87a6818b Mon Sep 17 00:00:00 2001
From: Pranav Anbarasu <pranavanba@gmail.com>
Date: Mon, 25 Sep 2023 23:26:50 +0000
Subject: [PATCH 1/3] Initial commit

---
 .gitignore | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 .gitignore

diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..80ca4a6
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,5 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+recover-pipeline-i2b2.Rproj

From 2c0b74f532b13b86965ca5b806fc300f25061c87 Mon Sep 17 00:00:00 2001
From: Pranav Anbarasu <pranavanba@gmail.com>
Date: Mon, 25 Sep 2023 23:32:45 +0000
Subject: [PATCH 2/3] Update function call to use new params required in
 updated function definition

---
 run-pipeline.R | 15 ++++++++++++++-
 1 file changed, 14 insertions(+), 1 deletion(-)

diff --git a/run-pipeline.R b/run-pipeline.R
index 4f0d5ce..8a3af16 100644
--- a/run-pipeline.R
+++ b/run-pipeline.R
@@ -10,5 +10,18 @@ dataset_name_filter <- Sys.getenv("DATASET_NAME_FILTER")
 concept_replacements <- eval(parse(text=Sys.getenv("CONCEPT_REPLACEMENTS")))
 concept_filter_col <- Sys.getenv("CONCEPT_FILTER_COL")
 synFolderID <- Sys.getenv("SYN_FOLDER_ID")
+method <- Sys.getenv("METHOD")
+s3bucket <- Sys.getenv("S3BUCKET")
+s3basekey <- Sys.getenv("S3BASEKEY")
+downloadLocation <- Sys.getenv("DOWNLOADLOCATION")
 
-recoverSummarizeR::summarize_pipeline(ontologyFileID, parquetDirID, dataset_name_filter, concept_replacements, concept_filter_col, synFolderID)
+recoverSummarizeR::summarize_pipeline(ontologyFileID, 
+                                      parquetDirID, 
+                                      dataset_name_filter, 
+                                      concept_replacements, 
+                                      concept_filter_col, 
+                                      synFolderID,
+                                      method,
+                                      s3bucket,
+                                      s3basekey,
+                                      downloadLocation)

From 975ee652aded054cf48cf567f42d4b7945b21bfe Mon Sep 17 00:00:00 2001
From: Pranav Anbarasu <pranavanba@gmail.com>
Date: Mon, 25 Sep 2023 23:32:52 +0000
Subject: [PATCH 3/3] Use Sage-Bionetworks repo

---
 Dockerfile | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 905d4c7..9a52b73 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -11,7 +11,7 @@ RUN R -e 'install.packages("synapser", repos = c("http://ran.synapse.org", "http
 RUN R -e 'install.packages("devtools")'
 RUN R -e 'devtools::install_github("Sage-Bionetworks/recoverSummarizeR")'
 
-RUN curl -o /root/run-pipeline.R https://raw.githubusercontent.com/pranavanba/recover-pipeline-i2b2/main/run-pipeline.R
+RUN curl -o /root/run-pipeline.R https://raw.githubusercontent.com/Sage-Bionetworks/recover-pipeline-i2b2/main/run-pipeline.R
 
 WORKDIR /root