add server specification

misc_scripts/README.md

@@ -21,7 +21,7 @@ Creates the `all_text` internal field in the biomarker collection used for the t
 
 ## peak_collection.py
 
-Let's you peak into one of the collections in the database. Currently is only setup for the `tst` server. When running the script, include the flag for the collection you want to peak into. You can only peak one collection at a time. You can also optionally pass in the `-n` argument to specify how many entries you want to view (by default the last 5 entries entered into the collection are returned).
+Let's you peak into one of the collections in the database. When running the script, include the flag for the collection you want to peak into. You can only peak one collection at a time. You can also optionally pass in the `-n` argument to specify how many entries you want to view (by default the last 5 entries entered into the collection are returned).
 
 Collection flags are as follows:
 
@@ -35,4 +35,4 @@ Collection flags are as follows:
 
 ## check_indexes.py
 
-Let's you check which indexes are currently setup in the target collection. Collection flags are as specified in the `peak_collection.py` file. Currently is only setup for the `tst` server.
+Let's you check which indexes are currently setup in the target collection. Collection flags are as specified in the `peak_collection.py` file.

misc_scripts/check_indexes.py

@@ -3,8 +3,9 @@
 import sys
 import argparse
 
-# test server port
-host = "mongodb://127.0.0.1:6061"
+host = "mongodb://127.0.0.1:"
+tst_port = "6061"
+prd_port = "7071"
 db_name = "biomarkerdb_api"
 db_user = "biomarkeradmin"
 db_pass = "biomarkerpass"
@@ -40,6 +41,7 @@ def print_indexes(collection: Collection):
 def main():
 
     parser = argparse.ArgumentParser(prog="peak_collection.py")
+    parser.add_argument("server", help="tst/prd")
     parser.add_argument(
         "-b",
         "--biomarker",
@@ -71,6 +73,11 @@ def main():
         help="Store true argument for the cache collection.",
     )
     options = parser.parse_args()
+    server = options.server.lower().strip()
+    if server not in {"tst", "prd"}:
+        print("Invalid server.")
+        sys.exit(1)
+    host_w_port = f"{host}{tst_port}" if server == "tst" else f"{host}{prd_port}"
     option_list = [
         options.biomarker,
         options.canonical_map,
@@ -90,7 +97,7 @@ def main():
 
     try:
         client = pymongo.MongoClient(
-            host,
+            host_w_port,
             username=db_user,
             password=db_pass,
             authSource=db_name,

misc_scripts/peak_collections.py

@@ -2,8 +2,9 @@
 import sys
 import argparse
 
-# test server port
-host = "mongodb://127.0.0.1:6061"
+host = "mongodb://127.0.0.1:"
+tst_port = "6061"
+prd_port = "7071"
 db_name = "biomarkerdb_api"
 db_user = "biomarkeradmin"
 db_pass = "biomarkerpass"
@@ -26,6 +27,7 @@
 def main():
 
     parser = argparse.ArgumentParser(prog="peak_collection.py")
+    parser.add_argument("server", help="tst/prd")
     parser.add_argument(
         "-b",
         "--biomarker",
@@ -58,6 +60,11 @@ def main():
     )
     parser.add_argument("-n", "--num", type=int, default=5)
     options = parser.parse_args()
+    server = options.server.lower().strip()
+    if server not in {"tst", "prd"}:
+        print("Invalid server.")
+        sys.exit(1)
+    host_w_port = f"{host}{tst_port}" if server == "tst" else f"{host}{prd_port}"
     option_list = [
         options.biomarker,
         options.canonical_map,
@@ -77,7 +84,7 @@ def main():
 
     try:
         client = pymongo.MongoClient(
-            host,
+            host_w_port,
             username=db_user,
             password=db_pass,
             authSource=db_name,