DEVSU-2797 - main.ipr_report - allow null ipr_url if ipr_upload = False

Author: dustinbleile

pori_python/ipr/main.py

@@ -31,8 +31,8 @@
     preprocess_cosmic,
     preprocess_expression_variants,
     preprocess_hla,
-    preprocess_msi,
     preprocess_hrd,
+    preprocess_msi,
     preprocess_signature_variants,
     preprocess_small_mutations,
     preprocess_structural_variants,
@@ -294,7 +294,7 @@ def ipr_report(
     username: str,
     password: str,
     content: Dict,
-    ipr_url: str,
+    ipr_url: str = "",
     log_level: str = "info",
     output_json_path: str = "",
     always_write_output_json: bool = False,
@@ -324,7 +324,7 @@ def ipr_report(
     Args:
         username: the username for connecting to GraphKB and IPR
         password: the password for connecting to GraphKB and IPR
-        ipr_url: base URL to use in connecting to IPR
+        ipr_url: base URL to use in connecting to IPR (eg. https://ipr-api.bcgsc.ca/api)
         log_level: the logging level
         content: report content
         output_json_path: path to a JSON file to output the report upload body.
@@ -358,17 +358,24 @@ def ipr_report(
     )
 
     # IPR CONNECTION
-    ipr_conn = IprConnection(username, password, ipr_url)
+    ipr_conn = None
+    if ipr_url:
+        ipr_conn = IprConnection(username, password, ipr_url)
+    else:
+        logger.warning("No ipr_url given")
 
     if validate_json:
+        if not ipr_conn:
+            raise ValueError("ipr_url required to validate_json")
         ipr_result = ipr_conn.validate_json(content)
         return ipr_result
 
     if upload_json:
+        if not ipr_conn:
+            raise ValueError("ipr_url required to validate_json")
         ipr_result = ipr_conn.upload_report(
             content, mins_to_wait, async_upload, ignore_extra_fields
         )
-        return ipr_result
 
     # validate the JSON content follows the specification
     try:
@@ -495,6 +502,8 @@ def ipr_report(
         comments_list.append(graphkb_comments)
 
     if include_ipr_variant_text:
+        if not ipr_conn:
+            raise ValueError("ipr_url required to include_ipr_variant_text")
         ipr_comments = get_ipr_analyst_comments(
             ipr_conn,
             gkb_matches,
@@ -550,18 +559,18 @@ def ipr_report(
 
     # if input includes hrdScore field, that is ok to pass to db
     # but prefer the 'hrd' field if it exists
-    if output.get('hrd'):
-        if output.get('hrd').get('score'):
-            output['hrdScore'] = output['hrd']['score']
-        output.pop('hrd')  # kbmatches have already been made
+    if output.get("hrd"):
+        if output.get("hrd").get("score"):
+            output["hrdScore"] = output["hrd"]["score"]
+        output.pop("hrd")  # kbmatches have already been made
 
-    ipr_spec = ipr_conn.get_spec()
-    output = clean_unsupported_content(output, ipr_spec)
     ipr_result = {}
     upload_error = None
 
     # UPLOAD TO IPR
     if ipr_upload:
+        ipr_spec = ipr_conn.get_spec()
+        output = clean_unsupported_content(output, ipr_spec)
         try:
             logger.info(f"Uploading to IPR {ipr_conn.url}")
             ipr_result = ipr_conn.upload_report(