Merge pull request #230 from umccr/dev

Hot fix - debug authentication issues
umccr · May 27, 2024 · 79341b9 · 79341b9
2 parents bbcd75a + 7ad155d
commit 79341b9
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Showing 6 changed files with 31 additions and 4 deletions.
diff --git a/Changelog.md b/Changelog.md
@@ -4,6 +4,15 @@ Changes in this log refer only to changes that make it to the 'main' branch. and
 
 For changes in deployment, please see the [deployment changelog](deploy/cttso-ica-to-pieriandx-cdk/Changelog.md) 
 
+## 2024-05-27
+
+> Author: Alexis Lucattini
+> Email: [Alexis.Lucattini@umccr.org](mailto:alexis.lucattini@umccr.org)
+
+### Hotfix
+
+* Debug authentication issues (https://github.com/umccr/cttso-ica-to-pieriandx/issues/229)
+
 ## 2024-05-06
 
 > Author: Alexis Lucattini

diff --git a/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md b/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md
@@ -3,6 +3,15 @@
 Changes in this log refer only to changes that make it to the 'main' branch and
 are nested under deploy/cttso-ica-to-pieriandx-cdk.  
 
+## 2024-05-27
+
+> Author: Alexis Lucattini
+> Email: [Alexis.Lucattini@umccr.org](mailto:alexis.lucattini@umccr.org)
+
+### Hotfix
+
+* Debug authentication issues (https://github.com/umccr/cttso-ica-to-pieriandx/issues/229)
+
 ## 2024-05-23
 
 > Author: Alexis Lucattini

diff --git a/deploy/cttso-ica-to-pieriandx-cdk/assets/cttso-ica-to-pieriandx-wrapper.sh b/deploy/cttso-ica-to-pieriandx-cdk/assets/cttso-ica-to-pieriandx-wrapper.sh
@@ -189,9 +189,12 @@ PIERIANDX_AWS_SECRET_ACCESS_KEY="$(
 # Collect the pieriandx access token
 # We assume that there is more than 5 minutes left on the clock
 while :; do
-  PIERIANDX_USER_AUTH_TOKEN="$(get_pieriandx_access_token)"
-  [[ -z "${PIERIANDX_USER_AUTH_TOKEN}" ]] || break
-  sleep 10
+  echo_stderr "Collecting PierianDx access token..."
+  if ! PIERIANDX_USER_AUTH_TOKEN="$(get_pieriandx_access_token)"; then
+      sleep 10
+  else
+      break
+  fi
 done
 
 # Export env vars

diff --git a/scripts/cttso-ica-to-pieriandx.py b/scripts/cttso-ica-to-pieriandx.py
@@ -3,6 +3,7 @@
 """
 Run sample on ICA to PierianDx
 """
+from __future__ import annotations
 
 from typing import Dict, Match
 from pathlib import Path

diff --git a/utils/accession.py b/utils/accession.py
@@ -85,6 +85,11 @@ def get_cases_df() -> pd.DataFrame:
         logger.debug("Printing response")
         if response is None:
             logger.warning(f"Trying again to get cases - attempt {iter_count}")
+            logger.warning(f"Client vars were: "
+                           f"'baseurl': {pyriandx_client.baseURL}, "
+                           f"'email': {pyriandx_client.headers['X-Auth-Email']}, "
+                           f"'institution': {pyriandx_client.headers['X-Auth-Institution']}, "
+                           f"'Token': {pyriandx_client.headers['X-Auth-Token'][:5]}***{pyriandx_client.headers['X-Auth-Token'][-5:]}")
             time.sleep(LIST_CASES_RETRY_TIME)
         else:
             break

diff --git a/utils/pieriandx_helper.py b/utils/pieriandx_helper.py
@@ -51,4 +51,4 @@ def get_pieriandx_client(email: str = environ.get("PIERIANDX_USER_EMAIL", None),
                   key=token,
                   institution=instiution,
                   base_url=base_url,
-                  key_is_auth_token=True)
+                  key_is_auth_token=True)