From 4e31d71793320f5411851a49bf8fbef886efb048 Mon Sep 17 00:00:00 2001
From: Long Trieu <longtrieujp@gmail.com>
Date: Tue, 18 Aug 2020 00:33:38 +0900
Subject: [PATCH] pubmed e2e

---
 pubmed.sh | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/pubmed.sh b/pubmed.sh
index 2939d0a..5aa42a3 100644
--- a/pubmed.sh
+++ b/pubmed.sh
@@ -96,13 +96,14 @@ elif [ "$TASK" = "brat" ]; then
     # brat
     cp -r $PRED_DIR $BRAT_DIR
 
-elif [ "$TASK" = "e2e pmid" ]; then
+elif [ "$TASK" = "e2e" ]; then
 
     echo "End-to-end event extraction"
     echo "--------------------------------"
     echo "1. Get text from PubMed ID"
 
-    PMID=$2
+    PM_TYPE=$2
+    PMID=$3
 
     TEXT_DIR="data/my-pubmed-$PMID/my-pubmed-$PMID-text/"
     python pubmed/pubmed2text.py $TASK $PMID $TEXT_DIR
@@ -121,8 +122,8 @@ elif [ "$TASK" = "e2e pmid" ]; then
     echo "--------------------------------"
     echo "3. Generate pubmed config"
 
-    MODEL_NAME=$3
-    GPU=$4
+    MODEL_NAME=$4
+    GPU=$5
     EXP_DIR="experiments/"
 
     python scripts/generate_configs.py $EXP_DIR $MY_DATA $MODEL_NAME $GPU