fixing issue of passing down parameters to function

uc-cdis · Aug 6, 2024 · 7ad0513 · 7ad0513
1 parent 7b85d38
commit 7ad0513
Showing 1 changed file with 23 additions and 25 deletions.
diff --git a/sidecar.sh b/sidecar.sh
@@ -9,15 +9,15 @@ function log(){
 }
 
 populate_notebook() {
-    MANIFEST=$1
+    MANIFEST_FILE=$1
     shift
     FOLDER=$1
     shift
     manifest_pull="!gen3  drs-pull manifest manifest.json"
     manifest_ls="!gen3 drs-pull ls manifest.json"
     jq --arg cmd "$manifest_ls" '.cells[1].source |= $cmd' "$FOLDER/data.ipynb" > "$FOLDER/data.tmp" && mv "$FOLDER/data.tmp" "$FOLDER/data.ipynb"
     jq --arg cmd "$manifest_pull" '.cells[3].source |= $cmd' "$FOLDER/data.ipynb" > "$FOLDER/data.tmp" && mv "$FOLDER/data.tmp" "$FOLDER/data.ipynb"
-    echo $MANIFEST | jq -c '.[]' | while read j; do
+    echo $MANIFEST_FILE | jq -c '.[]' | while read j; do
         obj=$(echo $j | jq -r .object_id)
         filename=$(echo $j | jq -r .file_name)
         filesize=$(echo $j | jq -r .file_size)
@@ -41,29 +41,29 @@ populate_notebook() {
 
 function populate() {
     log "querying manifest service at $GEN3_ENDPOINT/manifests/"
-    MANIFESTS=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/")
+    MANIFEST_FILE=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/")
     log "querying manifest service at $GEN3_ENDPOINT/metadata/"
-    METADATA=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/metadata/")
+    METADATA_FILE=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/metadata/")
 
-    while [ -z "$MANIFESTS" ] || [ -z "$METADATA" ]; do
-        if [ -z "$MANIFESTS" ]; then
+    while [ -z "$MANIFEST_FILE" ] && [ -z "$METADATA_FILE" ]; do
+        if [ -z "$MANIFEST_FILE" ]; then
             log "Unable to get manifests from '$GEN3_ENDPOINT/manifests/'"
-            log $MANIFESTS
+            log $MANIFEST_FILE
         fi
-        if [ -z "$METADATA" ]; then
+        if [ -z "$METADATA_FILE" ]; then
             log "Unable to get metadata from '$GEN3_ENDPOINT/metadata/'"
-            log $METADATA
+            log $METADATA_FILE
         fi
         log "sleeping for 15 seconds before trying again.."
         sleep 15
-        MANIFESTS=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/")
-        METADATA=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/metadata/")
+        MANIFEST_FILE=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/")
+        METADATA_FILE=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/metadata/")
     done
     log "successfully retrieved manifests and metadata for user"
 
     process_files() {
-        local data=$1
-        local base_dir=$2
+        local base_dir=$1
+        local data=$2
 
         echo $data | jq -c '.[]' | while read i; do
         FILENAME=$(echo "${i}" | jq -r .filename)
@@ -78,20 +78,22 @@ function populate() {
             chown -R 1000:100 $FOLDER
 
             if ["$base_dir" == "manifests"];then
-                MANIFEST=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/file/$FILENAME")
-                echo "${MANIFEST}" > $FOLDER/manifest.json
+                MANIFEST_FILE=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/file/$FILENAME")
+                echo "${MANIFEST_FILE}" > $FOLDER/manifest.json
                 log "Creating notebook for $FILENAME"
                 cp ./template_manifest.json $FOLDER/data.ipynb
-                populate_notebook "$MANIFEST" "$FOLDER"
+                populate_notebook "$MANIFEST_FILE" "$FOLDER"
             elif ["$base_dir" == "metadata"];then
-                METADATA=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/metadata/$FILENAME")
-                echo "${METADATA}" > $FOLDER/metadata.json
+                METADATA_FILE=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/metadata/$FILENAME")
+                echo "${METADATA_FILE}" > $FOLDER/metadata.json
             fi
         fi
         done
     }
-    echo $MANIFESTS | jq -c '.manifests' | process_files manifests
-    echo $METADATA | jq -c '.external_file_metadata' | process_files metadata
+    # echo $MANIFEST_FILE | jq -c '.manifests' | process_files manifests
+    process_files "manifests" "$(echo $MANIFEST_FILE | jq -c '.manifests')"
+    # echo $METADATA_FILE | jq -c '.external_file_metadata' | process_files metadata
+    process_files "metadata" "$(echo $METADATA_FILE | jq -c '.external_file_metadata')"
 
     # Make sure notebook user has write access to the folders
     chown -R 1000:100 /data
@@ -126,10 +128,6 @@ function get_access_token() {
     export ACCESS_TOKEN="$ACCESS_TOKEN"
 }
 
-function get_manifest_service_access_token() {
-    log "Getting access token"
-    ACCESS_TOKEN=$(curl -s -H "Content-Type: application/json" -X POST "https://$GEN3_ENDPOINT/user/credentials/api/access_token/" -d "{ \"api_key\": \"${API_KEY}\" }" | jq -r .access_token)
-}
 
 function mount_hatchery_files() {
     log "Mounting Hatchery files"
@@ -179,7 +177,7 @@ function main() {
     while true; do
         populate
         # If the access token expires, fetch a new access token and try again
-        if [[ $(echo "$MANIFESTS" | jq -r '.error') = "Please log in." ]]; then
+        if [[ $(echo "$MANIFEST_FILE" | jq -r '.error') = "Please log in." ]]; then
             echo "Session Expired. Trying again with new access token"
             get_access_token
         else