Feat/devsu 2797 remove gsc defaults dustin

pori_python/graphkb/util.py

@@ -222,6 +222,8 @@ def login_demo(self) -> None:
         1. get a first token from KeyCloak using username and password; self.login_demo()
         2. get a second token from the GraphKB API using keyCloakToken; self.login()
         """
+        if not self.url:
+            raise ValueError("no self.url set - cannot make a login demo")
         url_parts = urlsplit(self.url)
         base_url = f"{url_parts.scheme}://{url_parts.netloc}"
 
@@ -251,7 +253,8 @@ def login(self, username: str, password: str, pori_demo: bool = False) -> None:
         read_timeout = 61
 
         # KBDEV-1328. Alt. GraphKB login for GSC's PORI online demo
-        if pori_demo or "pori-demo" in self.url:
+        if self.url and (pori_demo or "pori-demo" in self.url):
+            logger.warning("login demo")
             self.login_demo()
 
         # use requests package directly to avoid recursion loop on login failure

pori_python/ipr/inputs.py

@@ -26,8 +26,8 @@
 from .constants import (
     COSMIC_SIGNATURE_VARIANT_TYPE,
     HLA_SIGNATURE_VARIANT_TYPE,
-    MSI_MAPPING,
     HRD_MAPPING,
+    MSI_MAPPING,
     TMB_SIGNATURE,
     TMB_SIGNATURE_VARIANT_TYPE,
 )

pori_python/ipr/ipr.py

@@ -168,7 +168,7 @@ def convert_statements_to_alterations(
         diseases = [c for c in statement["conditions"] if c["@class"] == "Disease"]
         disease_match = len(diseases) == 1 and diseases[0]["@rid"] in disease_matches
         reference = ";".join([e["displayName"] for e in statement["evidence"]])
-        if statement['relevance']['name'] == 'eligibility':
+        if statement["relevance"]["name"] == "eligibility":
             reference = ";".join([e["sourceId"] for e in statement["evidence"]])
 
         ipr_section = gkb_statement.categorize_relevance(

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.
@@ -358,13 +358,22 @@ def ipr_report(
     )
 
     # IPR CONNECTION
-    ipr_conn = IprConnection(username, password, ipr_url)
+    ipr_url = ipr_url if ipr_url else os.environ.get("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 upload_json")
         ipr_result = ipr_conn.upload_report(
             content, mins_to_wait, async_upload, ignore_extra_fields
         )
@@ -410,14 +419,15 @@ def ipr_report(
     )
 
     # GKB CONNECTION
+    gkb_user = graphkb_username if graphkb_username else username
+    gkb_pass = graphkb_password if graphkb_password else password
+    graphkb_url = graphkb_url if graphkb_url else os.environ.get("GRAPHKB_URL", "")
     if graphkb_url:
         logger.info(f"connecting to graphkb: {graphkb_url}")
         graphkb_conn = GraphKBConnection(graphkb_url)
     else:
-        graphkb_conn = GraphKBConnection()
-
-    gkb_user = graphkb_username if graphkb_username else username
-    gkb_pass = graphkb_password if graphkb_password else password
+        # graphkb_conn = GraphKBConnection()  # This will just error on trying to login
+        raise ValueError("graphkb_url is required")
 
     graphkb_conn.login(gkb_user, gkb_pass)
 
@@ -495,6 +505,8 @@ 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 +562,20 @@ 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:
+        if not ipr_conn:
+            raise ValueError("ipr_url required to upload_report")
+        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(

tests/test_graphkb/test_genes.py

@@ -7,6 +7,7 @@
 
 from pori_python.graphkb import GraphKBConnection
 from pori_python.graphkb.genes import (
+    PREFERRED_GENE_SOURCE_NAME,
     get_cancer_genes,
     get_cancer_predisposition_info,
     get_gene_information,
@@ -18,7 +19,6 @@
     get_pharmacogenomic_info,
     get_preferred_gene_name,
     get_therapeutic_associated_genes,
-    PREFERRED_GENE_SOURCE_NAME,
 )
 from pori_python.graphkb.util import get_rid
 

tests/test_ipr/test_inputs.py

@@ -7,8 +7,8 @@
 
 from pori_python.graphkb.match import INPUT_COPY_CATEGORIES
 from pori_python.ipr.constants import (
-    MSI_MAPPING,
     HRD_MAPPING,
+    MSI_MAPPING,
     TMB_SIGNATURE,
     TMB_SIGNATURE_HIGH_THRESHOLD,
 )
@@ -21,8 +21,8 @@
     preprocess_cosmic,
     preprocess_expression_variants,
     preprocess_hla,
-    preprocess_msi,
     preprocess_hrd,
+    preprocess_msi,
     preprocess_signature_variants,
     preprocess_small_mutations,
     preprocess_structural_variants,