Merge pull request #2 from Sage-Bionetworks/update-pipeline-script

Update pipeline script

.gitignore

@@ -0,0 +1,5 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata
+recover-pipeline-i2b2.Rproj

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
 

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)