Kpmp 4871 update validate args

README.md

@@ -24,7 +24,8 @@ To initialize the `.env` file, copy `wsi-worker/scripts/.env.example` and modify
 1. KPMP ID
 2. SVS filename without the `.svs` extension
 3. Package File ID from the Data Lake
-4. [Optional] stain type.  Values are 'he', 'pas', 'silver', 'tri', 'frz', 'tol' and 'cr'.  Defaults to 'pas'
+4. Slide type. Values are 'LM', 'EM', 'IF'.
+5. [Optional] stain type.  Values are 'he', 'pas', 'silver', 'tri', 'frz', 'tol' and 'cr'.  Defaults to 'pas'
 
 #### .env File
 1. `ENV_IMAGE`: defaults to `kingstonduo/wsi-worker`

docker/wsi-worker/svs2dz

@@ -3,7 +3,7 @@
 source /usr/sbin/svs2dz-functions.sh
 assert_no_errors "!!! source load failure"
 
-validate_args $1 $2 $3 $4
+validate_args $1 $2 $3 $4 $5
 # no assertion needed; validate_args works differently
 
 call_vips $1 $2 $3 $4

docker/wsi-worker/svs2dz-functions.sh

@@ -8,10 +8,10 @@ JOB_OUT_DIR=/data/job/out
 print_help() {
   cat << EOL
 --- Command help
-Usage: svs2dz "KPMP_ID" "FILENAME_NO_EXTENSION" "PKG_FILE_ID" ["STAIN_TYPE"]
+Usage: svs2dz "KPMP_ID" "FILENAME_NO_EXTENSION" "PKG_FILE_ID" "SLIDE_TYPE" ["STAIN_TYPE"]
 All arguments should be enclosed in double-quotes to escape spaces.
-Example: svs2dz "KPMP-Ex1" "KPMP-Ex1_TRI_1of1" "b9f7c729-8370-4f8d-9753-4a36e8ae57a4" "TRI"
-... The above example creates symlinks at <ENV_WSE_LINK_FROM_DIR>/files_KPMP-Ex1/KPMP-Ex1_TRI_1of1, stain type Trichrome
+Example: svs2dz "KPMP-Ex1" "KPMP-Ex1_TRI_1of1" "b9f7c729-8370-4f8d-9753-4a36e8ae57a4" "IF" "TRI"
+... The above example creates symlinks at <ENV_WSE_LINK_FROM_DIR>/files_KPMP-Ex1/KPMP-Ex1_TRI_1of1, slide type Immunofluorescence, stain type Trichrome
 EOL
 }
 
@@ -53,8 +53,12 @@ validate_args() {
   fi
 
   if [[ -z $4 ]]; then
+    print_error "!!! arg 4 must be slide type"
+  fi
+
+  if [[ -z $5 ]]; then
     echo "... optional stain not passed; defaulting to type 'pas'"
-    4=pas
+    5=pas
   fi
 
   if (( DID_ERROR > 0 )); then
@@ -111,5 +115,5 @@ extract_metadata() {
 }
 
 generate_mongo_records() {
-  node /usr/sbin/generate_mongo_records.js $1 $2 $3 $4 $JOB_OUT_DIR/metadata.json
+  node /usr/sbin/generate_mongo_records.js $1 $2 $3 $4 $5 $JOB_OUT_DIR/metadata.json
 }

scripts/run-wsi-worker.sh

@@ -9,7 +9,8 @@ mkdir -p ${ENV_LINK_DST_DIR_HOST}
 # arg $1 must be KPMP ID
 # arg $2 must be input file name (no extension) directly inside $JOB_IN_DIR
 # arg $3 must be file ID
-# arg $4 is currently optional stain type (defaults to "pas")
+# arg $4 must be stain type (LM, EM, IF)
+# arg $5 is currently optional stain type (defaults to "pas")
 
 docker run \
   --env-file .env \
@@ -18,4 +19,4 @@ docker run \
   -v ${ENV_LINK_DST_DIR_HOST}:${ENV_LINK_DST_DIR} \
   -v ${ENV_JOB_IN_DIR}:/data/job/in \
   -v ${ENV_JOB_OUT_DIR}:/data/job/out \
-  ${ENV_IMAGE} $1 $2 $3 $4
+  ${ENV_IMAGE} $1 $2 $3 $4 $5