Merge pull request #18 from uc-cdis/fix/if-cond

Fix/if cond

sidecar.sh

@@ -23,40 +23,36 @@ populate_notebook() {
         filesize=$(echo $j | jq -r .file_size)
 
         # Need to add a literal newline character that's why the quote is ending on next line
-        drs_pull="!gen3 drs-pull object $obj
-
-"
+        drs_pull="!gen3 drs-pull object $obj"
         # Need to add a literal newline character that's why the quote is ending on next line
-        jq --arg cmd "# File name: $filename - File size: $filesize
-" '.cells[5].source += [$cmd]' "$FOLDER/data.ipynb" > "$FOLDER/data.tmp"
+        jq --arg cmd "# File name: $filename - File size: $filesize" '.cells[5].source += [$cmd]' "$FOLDER/data.ipynb" > "$FOLDER/data.tmp"
         mv "$FOLDER/data.tmp" "$FOLDER/data.ipynb"
 
         jq --arg cmd "$drs_pull" '.cells[5].source += [$cmd]' "$FOLDER/data.ipynb" > "$FOLDER/data.tmp"
         mv "$FOLDER/data.tmp" "$FOLDER/data.ipynb"
 
-
     done
     log "Done populating notebook"
 }
 
 function populate() {
     log "querying manifest service at $GEN3_ENDPOINT/manifests"
-    MANIFEST=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests")
+    MANIFESTS=$(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/manifests/metadata")
 
-    while [ -z "$MANIFEST" ] && [ -z "$METADATA_FILE" ]; do
-        if [ -z "$MANIFEST" ]; then
-            log "Unable to get manifests from '$GEN3_ENDPOINT/manifests'"
-            log $MANIFEST
+    while [ -z "$MANIFESTS" ] && [ -z "$METADATA" ]; do
+        if [ -z "$MANIFESTS" ]; then
+            log "Unable to get manifests from '$GEN3_ENDPOINT/manifests/'"
+            log $MANIFESTS
         fi
-        if [ -z "$METADATA_FILE" ]; then
+        if [ -z "$METADATA" ]; then
             log "Unable to get metadata from '$GEN3_ENDPOINT/manifests/metadata'"
             log $METADATA
         fi
         log "sleeping for 15 seconds before trying again.."
         sleep 15
-        MANIFEST=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests")
+        MANIFESTS=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/")
         METADATA=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/metadata")
     done
     log "successfully retrieved manifests and metadata for user"
@@ -77,24 +73,25 @@ function populate() {
                 # make sure folder can be written to by notebook
                 chown -R 1000:100 $FOLDER
 
-                if [["$base_dir" == "manifests"]];then
+                if [[ "$base_dir" == "manifests" ]]; then
                     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_FILE" "$FOLDER"
-                elif [["$base_dir" == "metadata"]];then
+                elif [[ "$base_dir" == "metadata" ]]; then
                     METADATA_FILE=$(curl -s -H "Authorization: Bearer ${ACCESS_TOKEN}" "https://$GEN3_ENDPOINT/manifests/metadata/$FILENAME")
                     echo "${METADATA_FILE}" > $FOLDER/metadata.json
                 fi
             fi
         done
     }
-    if [ -n "$MANIFEST_FILE" ]; then
-        process_files "manifests" "$(echo $MANIFEST_FILE | jq -c '.manifests')"
+
+    if [ -n "$MANIFESTS" ]; then
+        process_files "manifests" "$(echo $MANIFESTS | jq -c '.manifests')"
     fi
-    if [ -n "$METADATA_FILE" ]; then
-        process_files "metadata" "$(echo $METADATA_FILE | jq -c '.external_file_metadata')"
+    if [ -n "$METADATA" ]; then
+        process_files "metadata" "$(echo $METADATA | jq -c '.external_file_metadata')"
     fi
 
     # Make sure notebook user has write access to the folders
@@ -175,11 +172,11 @@ function main() {
         mkdir "/data/${GEN3_ENDPOINT}/"
     fi
 
-    log "Trying to populate data from MDS..."
+    log "Trying to populate data from Manifest Service..."
     while true; do
         populate
         # If the access token expires, fetch a new access token and try again
-        if [[ $(echo "$MANIFEST" | jq -r '.error') = "Please log in." ]]; then
+        if [[ $(echo "$MANIFESTS" | jq -r '.error') = "Please log in." ]]; then
             echo "Session Expired. Trying again with new access token"
             get_access_token
         else