diff --git a/Changelog.md b/Changelog.md
index 633fb57..63e0d40 100644
--- 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) 
 
+## 2024-05-06
+
+> Author: Alexis Lucattini
+> Email: [Alexis.Lucattini@umccr.org](mailto:alexis.lucattini@umccr.org)
+
+### Documentation
+
+* Updated contribution guide (https://github.com/umccr/cttso-ica-to-pieriandx/pull/218)
+
 ## 2024-02-24
 
 > Author: Alexis Lucattini
diff --git a/README.md b/README.md
index 98b9612..2c06510 100644
--- a/README.md
+++ b/README.md
@@ -393,3 +393,12 @@ The accession csv will have the following columns (all columns are reduced to lo
 * Tumor Mutational Burden (Mutations/Mb) / tumor_mutational_burden_mutations_per_mb  # Optional (not used)
 * Percent Unstable Sites / percent_unstable_sites  # Optional (not used)
 * Percent Tumor Cell Nuclei in the Selected Areas / percent_tumor_cell_nuclei_in_the_selected_areas  # Optional (not used)
+
+## Contributing to this repository:
+
+Please make all changes in a separate branch and then create a PR to the `dev` branch. 
+
+A PR should then be made from the `dev` branch to the `main` branch.
+
+Please make sure you update the [Changelog.md](Changelog.md) file with your changes before making a PR into the main branch.
+If the changes are under the `deploy/cttso-ica-to-pieriandx-cdk` folder, please update the [deploy/cttso-ica-to-pieriandx-cdk/Changelog.md](deploy/cttso-ica-to-pieriandx-cdk/Changelog.md) file.
\ No newline at end of file
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md b/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md
index 74a3145..be9cbe4 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md
+++ b/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md
@@ -3,6 +3,34 @@
 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.  
 
+## 2024-05-07
+
+> Author: Alexis Lucattini
+> Email: [Alexis.Lucattini@umccr.org](mailto:alexis.lucattini@umccr.org)
+
+### Enhancements
+
+* Add ctTSO 1.2 portal run id to the LIMS sheet (https://github.com/umccr/cttso-ica-to-pieriandx/issues/216)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/222
+
+* Move to pieriandx infrastructure secret (https://github.com/umccr/cttso-ica-to-pieriandx/pull/221)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/220
+
+### Configuration Changes
+
+* Update project name mapping (https://github.com/umccr/cttso-ica-to-pieriandx/pull/217)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/215
+
+### Documentation
+
+* Add place to check if a sample has gone through pieriandx (https://github.com/umccr/cttso-ica-to-pieriandx/pull/218/files)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/213
+
+* Update links (https://github.com/umccr/cttso-ica-to-pieriandx/pull/217)
+  * Resolves https://github.com/umccr/cttso-ica-to-pieriandx/issues/214
+
+* Update manual launch optional parameters
+
 ## 2024-02-02
 
 > Author: Alexis Lucattini
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/README.md b/deploy/cttso-ica-to-pieriandx-cdk/README.md
index eb27e18..39635fd 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/README.md
+++ b/deploy/cttso-ica-to-pieriandx-cdk/README.md
@@ -18,6 +18,10 @@ AWS SSM Parameters for the dev pipeline stack can be found in _params-dev.json_.
 
 AWS SSM Parameters for the prod pipeline stack can be found in _params-prod.json_.
 
+The Production ctTSO LIMS sheet can be found [here][cttso_lims_link], you will need a UMCCR GSuite account to access it.  
+
+The ctTSO LIMS contains a list of samples that have been processed by the ctTSO pipeline and submitted to PierianDx.  
+
 ## Initialising the ctTSO LIMS
 
 If the lims sheet needs to be rebuilt, then the following steps may be of use.
@@ -53,6 +57,7 @@ new_headers = [
     "glims_needs_redcap",
     "redcap_sample_type",
     "redcap_is_complete",
+    "portal_run_id",
     "portal_wfr_id",
     "portal_wfr_end",
     "portal_wfr_status",
@@ -147,7 +152,7 @@ An example of the payloads file is as below:
 And then launch like so
 
 ```bash
-./scripts/launch_clinical_payloads --payloads-file "payloads.jsonl"
+./scripts/launch_clinical_payloads.sh --payloads-file "payloads.jsonl"
 ```
 
 Please note that the ica_workflow_run_id value is the "TSO_CTDNA_TUMOR_ONLY" workflow id. 
@@ -166,7 +171,7 @@ An example of the payloads file is as below:
 And then launch like so
 
 ```bash
-./scripts/launch_validation_payloads --payloads-file "payloads.jsonl"
+./scripts/launch_validation_payloads.sh --payloads-file "payloads.jsonl"
 ```
 
 ### ./scripts/wake_up_lambdas
@@ -359,6 +364,14 @@ This ssm parameter is NOT part of the cdk stack and MUST be updated using the sc
     "is_identified": "identified",
     "default_snomed_term": null
   },
+  {
+    "project_owner": "KSmith",
+    "project_name": "iPredict2",
+    "panel": "subpanel",
+    "sample_type": "patient_care_sample",
+    "is_identified": "identified",
+    "default_snomed_term":null
+  },
   {
     "project_owner": "*",
     "project_name": "*",
@@ -380,6 +393,16 @@ Regardless of panel type, payloads will in jsonl format with each line comprisin
 
 An example payloads file can be seen under [examples](examples/).
 
+Optional inputs for the payload include the following keys:
+
+* sample_type (patient_care_sample by default for clinical, validation for validation)
+* is_identified (identified by default for clinical, deidentified for validation 
+* panel_type: (subpanel by default for clinical, main for validation)
+* case_access_number: (must be in the format of `<subject_id>_<library_id>_001) 
+  * It is not recommended to set this, instead let the lambda generate this for you.
+* disease_name: "Disseminated malignancy of unknown primary" by default for validation. 
+  * For clinical, it is expected that this is set by RedCap.
+
 ### Running the command
 
 For validation samples, run the following command
@@ -408,9 +431,28 @@ because no identity-based policy allows the lambda:InvokeFunction action
 then it's likely a permissions issue. Please talk to your account administrator to elevate your permissions 
 before trying again.
 
+#### Checking a sample has gone through PierianDx 
+
+1. Check the ctTSO Lims, see if for a given subject id / library id combination, there is a pieriandx_case_id and pieriandx_case_accession_number
+2. Check [app.pieriandx.com][cgw_link] and see if the case is present
+3. View the AWS batch logs to see if the sample has been processed by AWS Batch
+    * [AWS Batch URL][aws_batch_url]
+    * Job Queue Name: cttso-ica-to-pieriandx-prod-batch-stack-jobqueue
+
+
+## Contributing to this repository (deployment):
+
+Please make all changes in a separate branch and then create a PR to the `dev` branch. 
+
+A PR should then be made from the `dev` branch to the `main` branch.
+
+Please update the [Changelog.md](Changelog.md) file before making a PR into the main branch.  
 
 [yawsso]:  https://github.com/victorskl/yawsso
 [aws_cli_v2]: https://docs.aws.amazon.com/cli/latest/userguide/getting-started-install.html
 [ica_ica_lazy]: https://github.com/umccr/ica-ica-lazy
 [git]: https://git-scm.com/
-[aws_umccr_wiki]: https://github.com/umccr/wiki/blob/master/computing/cloud/amazon/README.md
\ No newline at end of file
+[aws_umccr_wiki]: https://github.com/umccr/wiki/blob/master/computing/cloud/amazon/README.md
+[cttso_lims_link]: https://docs.google.com/spreadsheets/d/1Ev2aAYYwZQd9klCKyqON1Q17lBj49fb8dIwu0u5JivE
+[cgw_link]: https://app.pieriandx.com/
+[aws_batch_url]:  https://ap-southeast-2.console.aws.amazon.com/batch/home?region=ap-southeast-2
\ No newline at end of file
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
index 8b0d66a..4325a1a 100644
--- 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
@@ -13,6 +13,7 @@ CONTAINER_MEM     : The memory to assign to the container (for metric logging on
 '
 
 export AWS_DEFAULT_REGION="ap-southeast-2"
+PIERIANDX_ACCESS_TOKEN_LAMBDA_FUNCTION_NAME="collectPierianDxAccessToken"
 CLOUDWATCH_NAMESPACE="cttso-ica-to-pieriandx"
 CONTAINER_MOUNT_POINT="/work"
 METADATA_TOKEN=$(curl -X PUT "http://169.254.169.254/latest/api/token" -H "X-aws-ec2-metadata-token-ttl-seconds: 21600")
@@ -26,6 +27,35 @@ echo_stderr() {
   echo "$@" 1>&2
 }
 
+get_pieriandx_access_token() {
+  : '
+  Collect the PierianDx access token
+  '
+  local access_token_temp_file="$(mktemp access_token.XXX.json)"
+
+  # Run the lambda command to collect the access token
+  aws lambda invoke --function-name "${PIERIANDX_ACCESS_TOKEN_LAMBDA_FUNCTION_NAME}" "${access_token_temp_file}" 1>/dev/null
+
+  # Check if access_token_temp_file is empty
+  if [[ ! -s "${access_token_temp_file}" ]]; then
+    echo_stderr "Could not collect PierianDx access token"
+    return 1
+  fi
+
+  if [[ "$(jq --raw-output < "${access_token_temp_file}")" == "null" ]]; then
+    echo_stderr "Could not collect PierianDx access token, returned null, try again in a few moments"
+    return 1
+  fi
+
+  # Extract the access token
+  access_token="$( \
+    jq --raw-output '.auth_token' "${access_token_temp_file}" \
+  )"
+  rm -f "${access_token_temp_file}"
+
+  echo "${access_token}"
+}
+
 # Help function
 print_help(){
   echo "
@@ -134,25 +164,35 @@ job_output_dir="$(mktemp \
   "${CONTAINER_MOUNT_POINT}/${sample_name}.workdir.XXX")"
 
 # Create a job temp space
-job_temp_space="$(mktemp \
-  --directory \
-  "${CONTAINER_MOUNT_POINT}/${sample_name}.tmpspace.XXX")"
+job_temp_space="$( \
+  mktemp \
+    --directory \
+    "${CONTAINER_MOUNT_POINT}/${sample_name}.tmpspace.XXX" \
+)"
 
 # Set env vars
-ICA_ACCESS_TOKEN="$(aws secretsmanager get-secret-value --secret-id 'IcaSecretsPortal' | \
-                    jq --raw-output '.SecretString' \
-                  )"
+ICA_ACCESS_TOKEN="$( \
+  aws secretsmanager get-secret-value --secret-id 'IcaSecretsPortal' | \
+  jq --raw-output '.SecretString' \
+)"
 
 # Auth_tokens
-PIERIANDX_AWS_ACCESS_KEY_ID="$(aws secretsmanager get-secret-value --secret-id 'PierianDx/AWSAccessKeyID' | \
-                               jq --raw-output '.SecretString | fromjson | .PierianDxAWSAccessKeyID' \
-                              )"
-PIERIANDX_AWS_SECRET_ACCESS_KEY="$(aws secretsmanager get-secret-value --secret-id 'PierianDx/AWSSecretAccessKey' | \
-                                   jq --raw-output '.SecretString | fromjson | .PierianDxAWSSecretAccessKey' \
-                                 )"
-PIERIANDX_USER_AUTH_TOKEN="$(aws secretsmanager get-secret-value --secret-id 'PierianDx/UserAuthToken' | \
-                           jq --raw-output '.SecretString | fromjson | .PierianDxUserAuthToken' \
-                          )"
+PIERIANDX_AWS_ACCESS_KEY_ID="$(
+  aws secretsmanager get-secret-value --secret-id 'PierianDx/AWSAccessKeyID' | \
+  jq --raw-output '.SecretString | fromjson | .PierianDxAWSAccessKeyID' \
+)"
+PIERIANDX_AWS_SECRET_ACCESS_KEY="$(
+  aws secretsmanager get-secret-value --secret-id 'PierianDx/AWSSecretAccessKey' | \
+  jq --raw-output '.SecretString | fromjson | .PierianDxAWSSecretAccessKey' \
+)"
+
+# Collect the pieriandx access token
+# We assume that there is more than 5 minutes left on the clock
+while :; do
+  PIERIANDX_USER_AUTH_TOKEN="$(get_pieriandx_access_token)"
+  [[ -z "${PIERIANDX_USER_AUTH_TOKEN}" ]] || break
+  sleep 10
+done
 
 # Export env vars
 export ICA_ACCESS_TOKEN
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/constants.ts b/deploy/cttso-ica-to-pieriandx-cdk/constants.ts
index 7d19e1c..85226d1 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/constants.ts
+++ b/deploy/cttso-ica-to-pieriandx-cdk/constants.ts
@@ -39,11 +39,11 @@ export const GLIMS_SSM_PARAMETER_PATH: string = "/umccr/google/drive"
 export const SSM_LIMS_LAMBDA_FUNCTION_ARN_VALUE: string = "cttso-lims-update-and-launch-lambda-function"
 export const SSM_LIMS_LAMBDA_FUNCTION_EVENT_RULE_NAME_VALUE: string = "cttso-lims-update-and-launch-lambda-function-rule-name"
 
-// Token refresher things
-export const SSM_TOKEN_REFRESH_LAMBDA_FUNCTION_ARN_VALUE: string = "token-refresher-for-pieriandx-lambda-function"
-
 // Output things
 export const SSM_LAMBDA_FUNCTION_ARN_VALUE: string = "cttso-ica-to-pieriandx-lambda-function"
 
 // Project Owner mapping path
 export const SSM_PROJECT_NAME_TO_PIERIANDX_CONFIG_SSM_PATH: string = "cttso-lims-project-name-to-pieriandx-mapping"
+
+// Auth Token for PierianDx Lambda function name
+export const PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME: string = "collectPierianDxAccessToken"
\ No newline at end of file
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/lambda_code.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/lambda_code.py
index 3c6857f..f861e99 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/lambda_code.py
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/get_metadata_from_portal_and_defaults_and_launch_validation_workflow/lambda_code.py
@@ -124,12 +124,6 @@ def lambda_handler(event, context):
     # Get pieriandx case accession numbers
     pieriandx_case_accession_numbers: List = get_existing_pieriandx_case_accession_numbers()
 
-    # Get Case accession number
-    if (case_accession_number := event.get("case_accession_number", None)) is not None:
-        validate_case_accession_number(subject_id=subject_id,
-                                       library_id=library_id,
-                                       case_accession_number=case_accession_number)
-
     # Assign case accession number
     case_accession_number: str
     if (case_accession_number := event.get("case_accession_number", None)) is not None:
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/lambda_code.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/lambda_code.py
index 5aed03f..d618531 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/lambda_code.py
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/get_metadata_from_portal_and_redcap_and_launch_clinical_workflow/lambda_code.py
@@ -233,12 +233,6 @@ def lambda_handler(event, context):
     # Step 6 - check if case accession number is defined
     logger.info("Ensure that the case accession value does not already exist in PierianDx")
 
-    # Step 7 - Get Case accesison number
-    if (case_accession_number := event.get("case_accession_number", None)) is not None:
-        validate_case_accession_number(subject_id=subject_id,
-                                       library_id=library_id,
-                                       case_accession_number=case_accession_number)
-
     # Step 7 - Assign case accession number
     case_accession_number: str
     if (case_accession_number := event.get("case_accession_number", None)) is not None:
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py
index 8823418..2118c41 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/launch_available_payloads_and_update_cttso_lims_sheet/lambda_code.py
@@ -80,6 +80,7 @@ def merge_redcap_portal_and_glims_data(redcap_df, portal_df, glims_df) -> pd.Dat
       * subject_id
       * library_id
       * in_portal
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -105,6 +106,7 @@ def merge_redcap_portal_and_glims_data(redcap_df, portal_df, glims_df) -> pd.Dat
       * in_glims
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -167,6 +169,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -192,6 +195,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
     :return: A pandas dataframe with the following columns
       * subject_id
       * library_id
+      * portal_run_id
       * portal_wfr_id
       * panel
       * sample_type
@@ -205,6 +209,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
     processing_columns = [
         "subject_id",
         "library_id",
+        "portal_run_id",
         "portal_wfr_id",
         "panel",
         "sample_type",
@@ -233,6 +238,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
         f"  pieriandx_case_id.isnull() and "
         f"  ( pieriandx_submission_time.isnull() or pieriandx_submission_time < @one_week_ago ) and "
         f"  not in_pieriandx and "
+        f"  not portal_run_id.isnull() and "
         f"  not portal_wfr_id.isnull() and "
         f"  portal_wfr_status == 'Succeeded' and "
         f"  portal_is_failed_run == False and "
@@ -263,6 +269,7 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
         if not deleted_lims_df.query(
             f"subject_id == '{process_row['subject_id']}' and "
             f"library_id == '{process_row['library_id']}' and "
+            f"portal_run_id == '{process_row['portal_run_id']}' and "
             f"portal_wfr_id == '{process_row['portal_wfr_id']}'"
         ).shape[0] == 0:
             already_deleted_list_index.append(index)
@@ -291,13 +298,24 @@ def get_libraries_for_processing(merged_df) -> pd.DataFrame:
     ]
 
 
-def submit_library_to_pieriandx(subject_id: str, library_id: str, workflow_run_id: str, lambda_arn: str, panel_type: str, sample_type: str, is_identified: str, default_snomed_term: str):
+def submit_library_to_pieriandx(
+        subject_id: str,
+        library_id: str,
+        portal_run_id: str,
+        workflow_run_id: str,
+        lambda_arn: str,
+        panel_type: str,
+        sample_type: str,
+        is_identified: str,
+        default_snomed_term: str
+):
     """
     Submit library to pieriandx
     :param is_identified:
     :param sample_type:
     :param subject_id:
     :param library_id:
+    :param portal_run_id:
     :param workflow_run_id:
     :param lambda_arn:
     :param panel_type:
@@ -309,6 +327,7 @@ def submit_library_to_pieriandx(subject_id: str, library_id: str, workflow_run_i
     lambda_payload: Dict = {
             "subject_id": subject_id,
             "library_id": library_id,
+            "portal_run_id": portal_run_id,
             "ica_workflow_run_id": workflow_run_id,
             "panel_type": panel_type,
             "sample_type": sample_type,
@@ -366,6 +385,7 @@ def submit_libraries_to_pieriandx(processing_df: pd.DataFrame) -> pd.DataFrame:
     :param processing_df: A pandas dataframe with the following columns
       * subject_id
       * library_id
+      * portal_run_id
       * portal_wfr_id
       * panel
       * sample_type
@@ -377,6 +397,7 @@ def submit_libraries_to_pieriandx(processing_df: pd.DataFrame) -> pd.DataFrame:
       A pandas dataframe with the following columns
       * subject_id
       * library_id
+      * portal_run_id
       * portal_wfr_id
       * panel
       * sample_type
@@ -413,12 +434,13 @@ def submit_libraries_to_pieriandx(processing_df: pd.DataFrame) -> pd.DataFrame:
 
     for index, row in processing_df.iterrows():
         logger.info(f"Submitting the following subject id / library id to PierianDx")
-        logger.info(f"SubjectID='{row.subject_id}', LibraryID='{row.library_id}', Workflow Run ID='{row.portal_wfr_id}'")
+        logger.info(f"SubjectID='{row.subject_id}', LibraryID='{row.library_id}', Portal Run ID='{row.portal_run_id}', Workflow Run ID='{row.portal_wfr_id}'")
         logger.info(f"Submitted to arn: '{row.submission_arn}'")
         try:
             submit_library_to_pieriandx(
                 subject_id=row.subject_id,
                 library_id=row.library_id,
+                portal_run_id=row.portal_run_id,
                 workflow_run_id=row.portal_wfr_id,
                 lambda_arn=row.submission_arn,
                 panel_type=row.panel,
@@ -447,6 +469,7 @@ def append_to_cttso_lims(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame, e
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -479,6 +502,7 @@ def append_to_cttso_lims(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame, e
       * glims_needs_redcap
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -654,6 +678,7 @@ def get_pieriandx_incomplete_job_df_from_cttso_lims_df(cttso_lims_df: pd.DataFra
         * glims_is_identified
         * glims_default_snomed_term
         * glims_needs_redcap
+        * portal_run_id
         * portal_wfr_id
         * portal_wfr_end
         * portal_wfr_status
@@ -688,6 +713,7 @@ def get_pieriandx_incomplete_job_df_from_cttso_lims_df(cttso_lims_df: pd.DataFra
         * glims_is_identified
         * glims_default_snomed_term
         * glims_needs_redcap
+        * portal_run_id
         * portal_wfr_id
         * portal_wfr_end
         * portal_wfr_status
@@ -749,6 +775,7 @@ def update_merged_df_with_processing_df(merged_df, processing_df) -> pd.DataFram
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -768,6 +795,7 @@ def update_merged_df_with_processing_df(merged_df, processing_df) -> pd.DataFram
     :param processing_df: A pandas dataframe with the following columns
       * subject_id
       * library_id
+      * portal_run_id
       * portal_wfr_id
       * panel
       * sample_type
@@ -785,6 +813,7 @@ def update_merged_df_with_processing_df(merged_df, processing_df) -> pd.DataFram
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -848,6 +877,7 @@ def update_pieriandx_job_status_missing_df(pieriandx_job_status_missing_df, merg
       * glims_needs_redcap
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -872,6 +902,7 @@ def update_pieriandx_job_status_missing_df(pieriandx_job_status_missing_df, merg
       * glims_needs_redcap
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -892,6 +923,7 @@ def update_pieriandx_job_status_missing_df(pieriandx_job_status_missing_df, merg
         "in_pieriandx",
         "redcap_sample_type",
         "redcap_is_complete",
+        "portal_run_id",
         "portal_wfr_id",
         "portal_wfr_end",
         "portal_wfr_status",
@@ -929,6 +961,7 @@ def add_pieriandx_df_to_merged_df(merged_df: pd.DataFrame, pieriandx_df: pd.Data
       * in_glims
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -957,6 +990,7 @@ def add_pieriandx_df_to_merged_df(merged_df: pd.DataFrame, pieriandx_df: pd.Data
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1030,7 +1064,7 @@ def add_pieriandx_df_to_merged_df(merged_df: pd.DataFrame, pieriandx_df: pd.Data
 
     # Drop cases with pieriandx where duplicates have been created in id sections
     merged_df_with_pieriandx_df = merged_df_with_pieriandx_df.drop_duplicates(
-        subset=["subject_id", "library_id", "portal_wfr_id", "pieriandx_case_id"],
+        subset=["subject_id", "library_id", "portal_run_id", "portal_wfr_id", "pieriandx_case_id"],
         keep="last"
     )
 
@@ -1073,7 +1107,7 @@ def add_pieriandx_df_to_merged_df(merged_df: pd.DataFrame, pieriandx_df: pd.Data
     # Now that we've NAs a bunch of duplicates, lets group-by subject, library, portal wfr
     # And drop duplicates that have NA values for pieriandx case ids
     mini_dfs: List[pd.DataFrame] = []
-    for (subject_id, library_id, portal_wfr_id), mini_df in merged_df_with_pieriandx_df.groupby(["subject_id", "library_id", "portal_wfr_id"]):
+    for (subject_id, library_id, portal_run_id, portal_wfr_id), mini_df in merged_df_with_pieriandx_df.groupby(["subject_id", "library_id", "portal_run_id", "portal_wfr_id"]):
         if mini_df.shape[0] == 1:
             mini_dfs.append(mini_df)
             continue
@@ -1106,6 +1140,7 @@ def update_cttso_lims(update_df: pd.DataFrame, cttso_lims_df: pd.DataFrame, exce
       * glims_needs_redcap
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1130,6 +1165,7 @@ def update_cttso_lims(update_df: pd.DataFrame, cttso_lims_df: pd.DataFrame, exce
       * glims_needs_redcap
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1233,6 +1269,7 @@ def get_duplicate_case_ids(lims_df: pd.DataFrame) -> List:
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1291,10 +1328,11 @@ def get_duplicate_case_ids(lims_df: pd.DataFrame) -> List:
     # Append rows to drop
     subject_id: str
     library_id: str
+    portal_run_id: str
     portal_wfr_id: str
     mini_df: pd.DataFrame
-    for (subject_id, library_id, portal_wfr_id), mini_df in lims_df.groupby(
-            ["subject_id", "library_id", "portal_wfr_id"]):
+    for (subject_id, library_id, portal_run_id, portal_wfr_id), mini_df in lims_df.groupby(
+            ["subject_id", "library_id", "portal_run_id", "portal_wfr_id"]):
         # Check if it's just a single row
         if mini_df.shape[0] == 1:
             # Single unique row - nothing to see here
@@ -1315,6 +1353,7 @@ def get_duplicate_case_ids(lims_df: pd.DataFrame) -> List:
             logger.info(f"Got duplicates pieriandx case ids "
                         f"for subject_id '{subject_id}', "
                         f"library_id '{library_id}' and "
+                        f"portal_run_id '{portal_run_id}' and "
                         f"portal_wfr_id '{portal_wfr_id}'")
             continue
 
@@ -1405,6 +1444,7 @@ def cleanup_duplicate_rows(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame,
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1437,6 +1477,7 @@ def cleanup_duplicate_rows(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame,
       * glims_needs_redcap
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1468,6 +1509,7 @@ def cleanup_duplicate_rows(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame,
         * in_pieriandx
         * redcap_sample_type
         * redcap_is_complete
+        * portal_run_id
         * portal_wfr_id
         * portal_wfr_end
         * portal_wfr_status
@@ -1501,6 +1543,7 @@ def cleanup_duplicate_rows(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame,
         * glims_needs_redcap
         * redcap_sample_type
         * redcap_is_complete
+        * portal_run_id
         * portal_wfr_id
         * portal_wfr_end
         * portal_wfr_status
@@ -1529,7 +1572,7 @@ def cleanup_duplicate_rows(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame,
     # Merge our dataframes so we only need to do this once
     merged_lims_df: pd.DataFrame = pd.merge(
         merged_df, cttso_lims_df,
-        on=["subject_id", "library_id", "portal_wfr_id", "pieriandx_case_id"],
+        on=["subject_id", "library_id", "portal_run_id", "portal_wfr_id", "pieriandx_case_id"],
         how="outer", suffixes=("", "_lims")
     )
 
@@ -1547,7 +1590,7 @@ def cleanup_duplicate_rows(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFrame,
     # Iterate again through the lims df and drop any duplicates now where pieriandx case id is null
     # And another pieriandx case id exists
     mini_dfs: List[pd.DataFrame] = []
-    for (subject_id, library_id, portal_wfr_id), mini_df in cttso_lims_df_dedup.groupby(["subject_id", "library_id", "portal_wfr_id"]):
+    for (subject_id, library_id, portal_run_id, portal_wfr_id), mini_df in cttso_lims_df_dedup.groupby(["subject_id", "library_id", "portal_run_id", "portal_wfr_id"]):
         if mini_df.shape[0] == 1:
             mini_dfs.append(mini_df)
             continue
@@ -1601,17 +1644,19 @@ def get_pieriandx_case_id_from_merged_df_for_pending_case(cttso_lims_series, mer
 
     subject_id: str = cttso_lims_series['subject_id']
     library_id: str = cttso_lims_series['library_id']
+    portal_run_id: str = cttso_lims_series['portal_run_id']
     portal_wfr_id: str = cttso_lims_series['portal_wfr_id']
 
     merged_rows = merged_df.query(
         f"subject_id=='{subject_id}' and "
         f"library_id=='{library_id}' and "
+        f"portal_run_id=='{portal_run_id}' and "
         f"portal_wfr_id=='{portal_wfr_id}'"
     )
 
     # Check we've gotten just one row
     if merged_rows.shape[0] == 0:
-        logger.warning(f"Subject '{subject_id}', library '{library_id}', '{portal_wfr_id}' cannot be found in merged df")
+        logger.warning(f"Subject '{subject_id}', library '{library_id}', '{portal_run_id}', '{portal_wfr_id}' cannot be found in merged df")
         return None
     if merged_rows.shape[0] > 1:
         # Returning the 'latest' id makes sense but what if it hasn't been created yet
@@ -1647,6 +1692,7 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1679,6 +1725,7 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
       * glims_needs_redcap
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1706,6 +1753,7 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1756,7 +1804,7 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
     cttso_lims_df_valid_merge = cttso_lims_df.query(
         "not pieriandx_case_id.isnull() and "
         "not pieriandx_submission_time.isnull() "
-    )[["subject_id", "library_id", "portal_wfr_id", "pieriandx_case_id", "pieriandx_submission_time"]].drop_duplicates()
+    )[["subject_id", "library_id", "portal_run_id", "portal_wfr_id", "pieriandx_case_id", "pieriandx_submission_time"]].drop_duplicates()
 
     cttso_lims_df_with_valid_case_id = cttso_lims_df_valid_merge.query(
         "pieriandx_case_id.str.isdigit()",
@@ -1781,14 +1829,14 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
     merged_lims_df_valid = pd.merge(
         merged_df, cttso_lims_df_with_valid_case_id,
         how="left",
-        on=["subject_id", "library_id", "portal_wfr_id", "pieriandx_case_id"]
+        on=["subject_id", "library_id", "portal_run_id", "portal_wfr_id", "pieriandx_case_id"]
     )
 
     # Join pieriandx submission time for merged_lims_df where pieriandx_submission_time is null?
     merged_lims_df_invalid = pd.merge(
         merged_df, cttso_lims_df_without_valid_case_id,
         how="left",
-        on=["subject_id", "library_id", "portal_wfr_id"],
+        on=["subject_id", "library_id", "portal_run_id", "portal_wfr_id"],
         suffixes=("_merged", "_lims")
     )
 
@@ -1828,8 +1876,8 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
         # Case 2
         elif pd.isnull(pieriandx_case_id_merged) and pieriandx_case_id_lims == 'pending':
             # Check sample submission time is not too old
-            logger.info(f"Got 'pending' case id for sample subject / library / portal "
-                        f"{row['subject_id']}, {row['library_id']} {row['portal_wfr_id']} "
+            logger.info(f"Got 'pending' case id for sample subject / library / portal run / portal wfr "
+                        f"{row['subject_id']}, {row['library_id']} {row['portal_run_id']} {row['portal_wfr_id']} "
                         f"but never got a matching pieriandx accession number")
             one_week_ago = (datetime.utcnow() - timedelta(days=7)).date()
 
@@ -1871,12 +1919,12 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
             merged_lims_df_invalid
         ],
         ignore_index=True
-    )[["subject_id", "library_id", "portal_wfr_id", "pieriandx_case_id", "pieriandx_submission_time"]]
+    )[["subject_id", "library_id", "portal_run_id", "portal_wfr_id", "pieriandx_case_id", "pieriandx_submission_time"]]
 
     # Drop duplicates but fill pieriandx submission time
     new_rows = []
-    for (subject_id, library_id, portal_wfr_id, pieriandx_case_id), time_df in merged_lims_df_valid_and_invalid_df.groupby(
-        ["subject_id", "library_id", "portal_wfr_id", "pieriandx_case_id"]
+    for (subject_id, library_id, portal_run_id, portal_wfr_id, pieriandx_case_id), time_df in merged_lims_df_valid_and_invalid_df.groupby(
+        ["subject_id", "library_id", "portal_run_id", "portal_wfr_id", "pieriandx_case_id"]
     ):
         if time_df.shape[0] == 1:
             new_rows.append(time_df)
@@ -1892,7 +1940,7 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
         new_rows.append(
             time_df.drop_duplicates(
                 subset=[
-                    "subject_id", "library_id",
+                    "subject_id", "library_id", "portal_run_id",
                     "portal_wfr_id", "pieriandx_case_id"
                 ],
                 keep="first"
@@ -1908,7 +1956,7 @@ def bind_pieriandx_case_submission_time_to_merged_df(merged_df: pd.DataFrame, ct
     merged_lims_df = merged_df.merge(
         merged_lims_df_valid_and_invalid_df,
         how="left",
-        on=["subject_id", "library_id", "portal_wfr_id", "pieriandx_case_id"]
+        on=["subject_id", "library_id", "portal_run_id", "portal_wfr_id", "pieriandx_case_id"]
     )
 
     return merged_lims_df
@@ -1927,6 +1975,7 @@ def drop_to_be_deleted_cases(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFram
       * in_pieriandx
       * redcap_sample_type
       * redcap_is_complete
+      * portal_run_id
       * portal_wfr_id
       * portal_wfr_end
       * portal_wfr_status
@@ -1960,6 +2009,7 @@ def drop_to_be_deleted_cases(merged_df: pd.DataFrame, cttso_lims_df: pd.DataFram
         * glims_needs_redcap
         * redcap_sample_type
         * redcap_is_complete
+        * portal_run_id
         * portal_wfr_id
         * portal_wfr_end
         * portal_wfr_status
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/globals.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/globals.py
index 1ffbaa9..d584977 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/globals.py
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/globals.py
@@ -44,8 +44,7 @@ class SampleType(Enum):
 
 PIERIANDX_USER_EMAIL_SSM_PARAMETER_PATH = "/cdk/cttso-ica-to-pieriandx/env_vars/pieriandx_user_email"
 PIERIANDX_INSTITUTION_SSM_PARAMETER_PATH = "/cdk/cttso-ica-to-pieriandx/env_vars/pieriandx_institution"
-PIERIANDX_USER_AUTH_TOKEN_SECRETS_MANAGER_PATH = "PierianDx/UserAuthToken"
-PIERIANDX_USER_AUTH_TOKEN_SECRETS_MANAGER_KEY = "PierianDxUserAuthToken"
+PIERIANDX_USER_AUTH_TOKEN_LAMBDA_PATH = "collectPierianDxAccessToken"
 
 PIERIANDX_CDK_SSM_PATH: Path = Path("/cdk") / "cttso-ica-to-pieriandx" / "env_vars"
 PIERIANDX_CDK_SSM_LIST: List = [
@@ -54,9 +53,6 @@ class SampleType(Enum):
     "PIERIANDX_BASE_URL"
 ]
 
-PIERIANDX_USER_AUTH_TOKEN_SECRETS_PATH: Path = Path("PierianDx") / "UserAuthToken"
-PIERIANDX_USER_AUTH_TOKEN_SECRETS_KEY: str = "PierianDxUserAuthToken"
-
 PIERIANDX_LAMBDA_LAUNCH_FUNCTION_ARN_SSM_PATH = "cttso-ica-to-pieriandx-lambda-function"
 
 LIMS_PROJECT_NAME_MAPPING_SSM_PATH = "cttso-lims-project-name-to-pieriandx-mapping"
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/gspread_helpers.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/gspread_helpers.py
index 6526467..ed11304 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/gspread_helpers.py
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/gspread_helpers.py
@@ -211,6 +211,7 @@ def get_cttso_lims() -> (pd.DataFrame, pd.DataFrame):
         * glims_needs_redcap
         * redcap_sample_type
         * redcap_is_complete
+        * portal_run_id
         * portal_wfr_id
         * portal_wfr_end
         * portal_wfr_status
@@ -291,6 +292,7 @@ def get_deleted_lims_df() -> (pd.DataFrame, pd.DataFrame):
         * redcap_sample_type
         * redcap_is_complete
         * portal_wfr_id
+        * portal_run_id
         * portal_wfr_end
         * portal_wfr_status
         * portal_sequence_run_name
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/pieriandx_helpers.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/pieriandx_helpers.py
index 2b9b5bb..e880cf4 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/pieriandx_helpers.py
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/pieriandx_helpers.py
@@ -7,6 +7,8 @@
 import os
 import re
 from typing import Tuple, Dict, List, Union
+
+from mypy_boto3_lambda import LambdaClient
 from pyriandx.client import Client
 import json
 import pandas as pd
@@ -17,17 +19,15 @@
 from .globals import \
     PIERIANDX_CDK_SSM_LIST, \
     PIERIANDX_CDK_SSM_PATH, \
-    PIERIANDX_USER_AUTH_TOKEN_SECRETS_MANAGER_PATH, \
-    PIERIANDX_USER_AUTH_TOKEN_SECRETS_MANAGER_KEY, \
     MAX_ATTEMPTS_GET_CASES, LIST_CASES_RETRY_TIME, \
-    PanelType, SampleType
+    PanelType, SampleType, PIERIANDX_USER_AUTH_TOKEN_LAMBDA_PATH
 
 from .miscell import \
     change_case
 
 from .aws_helpers import \
     SSMClient, get_boto3_ssm_client, \
-    SecretsManagerClient, get_boto3_secretsmanager_client
+    get_boto3_lambda_client
 
 from .logger import get_logger
 
@@ -75,22 +75,24 @@ def get_pieriandx_env_vars() -> Tuple:
 
         output_dict[env_var] = parameter_value
 
-    # Set PIERIANDX_USER_PASSWORD based on secret
+    # Set PIERIANDX_USER_AUTH_TOKEN based on secret
     if "PIERIANDX_USER_AUTH_TOKEN" in os.environ:
         # Already here!
         output_dict["PIERIANDX_USER_AUTH_TOKEN"] = os.environ["PIERIANDX_USER_AUTH_TOKEN"]
     else:
         # Get the secrets manager client
-        secrets_manager_client: SecretsManagerClient = get_boto3_secretsmanager_client()
-        response = secrets_manager_client.get_secret_value(
-            SecretId=str(PIERIANDX_USER_AUTH_TOKEN_SECRETS_MANAGER_PATH)
-        )
-        secrets_json = json.loads(response.get("SecretString"))
-        if PIERIANDX_USER_AUTH_TOKEN_SECRETS_MANAGER_KEY not in secrets_json.keys():
-            logger.error(f"Could not find secrets key in {PIERIANDX_USER_AUTH_TOKEN_SECRETS_MANAGER_PATH}")
-            raise ValueError
-
-        output_dict["PIERIANDX_USER_AUTH_TOKEN"] = secrets_json[PIERIANDX_USER_AUTH_TOKEN_SECRETS_MANAGER_KEY]
+        lambda_client: LambdaClient = get_boto3_lambda_client()
+
+        # Collect the auth token
+        auth_token_resp = None
+        while auth_token_resp is None or auth_token_resp == 'null' or json.loads(auth_token_resp).get("auth_token") is None:
+            response = lambda_client.invoke(
+                FunctionName=PIERIANDX_USER_AUTH_TOKEN_LAMBDA_PATH,
+                InvocationType="RequestResponse"
+            )
+            auth_token_resp = response['Payload'].read().decode('utf-8')
+
+        output_dict["PIERIANDX_USER_AUTH_TOKEN"] = json.loads(auth_token_resp).get("auth_token")
 
     return (
         output_dict.get("PIERIANDX_USER_EMAIL"),
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/portal_helpers.py b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/portal_helpers.py
index 9dd46d9..ce3babd 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/portal_helpers.py
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/lambda_utils/portal_helpers.py
@@ -115,7 +115,8 @@ def get_portal_workflow_run_data_df() -> pd.DataFrame:
     :return: A pandas DataFrame with the following columns
       * subject_id
       * library_id
-      * portal_wfr_id
+      * portal_run_id                 -> The portal run ID
+      * portal_wfr_id                 -> The ICA workflow run ID
       * portal_wfr_end                -> The end timestamp of the workflow
       * portal_wfr_status             -> The status of the workflow run
       * portal_sequence_run_name      -> The sequence run name from this cttso sample
@@ -259,11 +260,12 @@ def get_portal_workflow_run_data_df() -> pd.DataFrame:
         [
             "subject_id",
             "library_id",
+            "portal_run_id",
             "portal_wfr_id",
             "portal_wfr_end",
             "portal_wfr_status",
             "portal_sequence_run_name",
-            "portal_is_failed_run"""
+            "portal_is_failed_run"
         ]
     ]
 
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/Dockerfile b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/Dockerfile
deleted file mode 100644
index 2d00eb7..0000000
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/Dockerfile
+++ /dev/null
@@ -1,52 +0,0 @@
-FROM public.ecr.aws/lambda/provided:al2
-
-# Args
-ARG CURL_VERSION="7.84.0"
-
-# Copy in bootstrap and function script
-COPY bootstrap ${LAMBDA_RUNTIME_DIR}
-COPY function.sh ${LAMBDA_TASK_ROOT}
-
-# Convert to executables
-RUN chmod 755 ${LAMBDA_RUNTIME_DIR}/bootstrap && \
-    chmod 755 ${LAMBDA_TASK_ROOT}/function.sh
-
-# Install the absolute latest version of curl
-RUN yum update -y && \
-    yum install -y \
-      libssl-dev \
-      autoconf \
-      libtool \
-      make \
-      jq \
-      wget \
-      gzip \
-      unzip \
-      openssl \
-      less \
-      openssl-devel && \
-    echo "Installing latest version of curl" 1>&2 && \
-    rm /usr/bin/curl && \
-    wget "https://curl.se/download/curl-${CURL_VERSION}.tar.gz" && \
-    tar -xf curl-${CURL_VERSION}.tar.gz && \
-    ( \
-      cd curl-${CURL_VERSION}/ && \
-      autoreconf -fi && \
-      ./configure \
-        --disable-static \
-        --with-ssl \
-        --prefix / && \
-      make && \
-      make install \
-    ) && \
-    rm "curl-${CURL_VERSION}.tar.gz" && \
-    rm -rf curl-${CURL_VERSION}/ && \
-    echo "Installing the latest version of aws binary" 1>&2 && \
-    curl --silent --output "awscliv2.zip" \
-      "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" && \
-    unzip -qq "awscliv2.zip" && \
-    ./aws/install && \
-    rm "awscliv2.zip" && \
-    rm -rf "aws/"
-
-CMD ["function.handler"]
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/bootstrap b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/bootstrap
deleted file mode 100644
index 326f0b0..0000000
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/bootstrap
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/sh
-
-set -euo pipefail
-
-# Initialization - load function handler
-source $LAMBDA_TASK_ROOT/"$(echo $_HANDLER | cut -d. -f1).sh"
-
-# Processing
-while true
-do
-  HEADERS="$(mktemp)"
-  # Get an event. The HTTP request will block until one is received
-  EVENT_DATA=$(curl -sS -LD "$HEADERS" -X GET "http://${AWS_LAMBDA_RUNTIME_API}/2018-06-01/runtime/invocation/next")
-
-  # Extract request ID by scraping response headers received above
-  REQUEST_ID=$(grep -Fi Lambda-Runtime-Aws-Request-Id "$HEADERS" | tr -d '[:space:]' | cut -d: -f2)
-
-  # Run the handler function from the script
-  RESPONSE=$($(echo "$_HANDLER" | cut -d. -f2) "$EVENT_DATA")
-
-  # Send the response
-  curl -X POST "http://${AWS_LAMBDA_RUNTIME_API}/2018-06-01/runtime/invocation/$REQUEST_ID/response"  -d "$RESPONSE"
-done
\ No newline at end of file
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/function.sh b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/function.sh
deleted file mode 100644
index e12ce8a..0000000
--- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/token_refresher/function.sh
+++ /dev/null
@@ -1,117 +0,0 @@
-#!/usr/bin/env bash
-
-set -euo pipefail
-
-# Set globals
-TOKEN_SECRET_ID="PierianDx/UserAuthToken"
-
-# Set preliminary functions
-get_aws_ssm_parameter () {
-  # Get AWS SSM Parameter
-  local ssm_parameter_path="$1"
-    aws ssm get-parameter \
-    --output json \
-    --name "${ssm_parameter_path}" | \
-  jq --raw-output \
-    '.Parameter.Value'
-}
-
-# Set glocals
-
-# Get values
-SERVICE_URL="$( \
-  get_aws_ssm_parameter "/cdk/cttso-ica-to-pieriandx/env_vars/pieriandx_base_url"
-)"
-SERVICE_USERNAME="$( \
-  get_aws_ssm_parameter "/cdk/cttso-ica-to-pieriandx/env_vars/pieriandx_user_email"
-)"
-SERVICE_INSTITUTION="$( \
-  get_aws_ssm_parameter "/cdk/cttso-ica-to-pieriandx/env_vars/pieriandx_institution"
-)"
-SERVICE_PASSWORD="$( \
-  aws secretsmanager get-secret-value \
-    --output json \
-    --secret-id 'PierianDx/UserPassword' | \
-  jq --raw-output \
-    '
-      .SecretString |
-      fromjson |
-      .PierianDxUserPassword
-    ' \
-)"
-
-LOGIN_URL="${SERVICE_URL}/login"
-
-function handler () {
-  auth_token="$( \
-    curl \
-      --fail \
-      --silent \
-      --location \
-      --request GET "${LOGIN_URL}" \
-      --header "Accept: application/json" \
-      --header "X-Auth-Email: ${SERVICE_USERNAME}" \
-      --header "X-Auth-Key: ${SERVICE_PASSWORD}" \
-      --header "X-Auth-Institution: ${SERVICE_INSTITUTION}" \
-      --write-out "%header{X-Auth-Token}" \
-  )"
-
-  # Failure
-  if [[ -z "${auth_token}" ]]; then
-    echo "Error! Couldn't get authentication token"
-    exit 1
-  fi
-
-  # Get secret as a json string
-  input_secret_json_str="$( \
-    jq \
-      --null-input \
-      --raw-output \
-      --compact-output \
-      --arg auth_token "${auth_token}" \
-      '
-        {
-          "PierianDxUserAuthToken": $auth_token
-        }
-      '
-  )"
-
-  # Check secret exists 0 for false, 1 for true
-  secret_exists="$( \
-    aws secretsmanager list-secrets \
-      --output json \
-      --filters "$( \
-        jq --null-input --raw-output \
-          '
-            [
-              {
-                "Key": "name",
-                "Values": [
-                  "PierianDx/UserAuthToken"
-                ]
-              }
-            ]
-          ' \
-      )" | \
-    jq --raw-output \
-      '
-        .SecretList | length
-      ' \
-  )"
-
-  if [[ "${secret_exists}" == "1" ]]; then
-      # Just update the secret
-      echo "Updating token" 1>&2
-      aws secretsmanager update-secret \
-        --secret-id "${TOKEN_SECRET_ID}" \
-        --secret-string "${input_secret_json_str}"
-  else
-      echo "Creating secret and token" 1>&2
-      aws secretsmanager create-secret \
-        --name "${TOKEN_SECRET_ID}" \
-        --secret-string "${input_secret_json_str}"
-  fi
-
-  echo "Successfully created/updated token" 1>&2
-
-}
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-batch-stack.ts b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-batch-stack.ts
index 1e22034..b10bbc0 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-batch-stack.ts
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-batch-stack.ts
@@ -54,8 +54,12 @@ import {
     SSM_LAMBDA_FUNCTION_ARN_VALUE,
     DATA_PORTAL_API_ID_SSM_PARAMETER,
     SECRETS_MANAGER_PIERIANDX_PATH,
-    SECRETS_MANAGER_ICA_SECRETS_PATH, SSM_PIERIANDX_PATH, DATA_PORTAL_API_DOMAIN_NAME_SSM_PARAMETER
+    SECRETS_MANAGER_ICA_SECRETS_PATH,
+    SSM_PIERIANDX_PATH,
+    DATA_PORTAL_API_DOMAIN_NAME_SSM_PARAMETER,
+    PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME
 } from "../constants";
+import {Lambda} from "aws-cdk-lib/aws-ses-actions";
 
 
 interface CttsoIcaToPieriandxBatchStackProps extends StackProps {
@@ -156,6 +160,14 @@ export class CttsoIcaToPieriandxBatchStack extends Stack {
             )
         )
 
+        // Allow batch instance role to invoke the collect Pieriandx Access Token Function
+        const pieriandx_access_token_lambda_obj = LambdaFunction.fromFunctionName(
+            this,
+            'pieriandx-access-token-lambda',
+            PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME
+        )
+        pieriandx_access_token_lambda_obj.grantInvoke(batch_instance_role)
+
         // Add ICA secrets access to batch instance role
         const ica_secrets_path = Secret.fromSecretNameV2(
             this,
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-lims-maker-lambda-stack.ts b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-lims-maker-lambda-stack.ts
index b2678ec..201e462 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-lims-maker-lambda-stack.ts
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-lims-maker-lambda-stack.ts
@@ -18,10 +18,11 @@ import {
     GLIMS_SSM_PARAMETER_PATH,
     REDCAP_LAMBDA_FUNCTION_SSM_KEY,
     SSM_LIMS_LAMBDA_FUNCTION_EVENT_RULE_NAME_VALUE,
-    SSM_PROJECT_NAME_TO_PIERIANDX_CONFIG_SSM_PATH
+    SSM_PROJECT_NAME_TO_PIERIANDX_CONFIG_SSM_PATH, PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME
 } from "../constants";
 import {Rule, Schedule} from "aws-cdk-lib/aws-events";
 import { LambdaFunction as LambdaFunctionTarget } from "aws-cdk-lib/aws-events-targets"
+import {Function as LambdaFunction} from "aws-cdk-lib/aws-lambda";
 
 
 interface CttsoIcaToPieriandxLimsMakerLambdaStackProps extends StackProps {
@@ -266,7 +267,13 @@ export class CttsoIcaToPieriandxLimsMakerLambdaStack extends Stack {
             })
         )
 
-        // Step 4: Add ssm access to get Rule
+        // Allow secret collection
+        const pieriandx_access_token_lambda_obj = LambdaFunction.fromFunctionName(
+            this,
+            'pieriandx-access-token-lambda',
+            PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME
+        )
+        pieriandx_access_token_lambda_obj.grantInvoke(<Role>lambda_function.role)
 
 
         // Create a rule to trigger this lambda
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-pipeline-stack.ts b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-pipeline-stack.ts
index c3542e7..4c30fbd 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-pipeline-stack.ts
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-pipeline-stack.ts
@@ -9,7 +9,6 @@ import { LinuxBuildImage } from "aws-cdk-lib/aws-codebuild";
 import { CodeBuildStep } from "aws-cdk-lib/pipelines";
 import {CttsoIcaToPieriandxRedcapLambdaStage} from "./cttso-ica-to-pieriandx-redcap-lambda-stage";
 import {CttsoIcaToPieriandxValidationLambdaStage} from "./cttso-ica-to-pieriandx-validation-lambda-stage";
-import {CttsoIcaToPieriandxTokenRefreshLambdaStage} from "./cttso-ica-to-pieriandx-token-refresher-lambda-stage";
 import {CttsoIcaToPieriandxLimsMakerLambdaStage} from "./cttso-ica-to-pieriandx-lims-make-stage";
 
 
@@ -132,21 +131,6 @@ export class CttsoIcaToPieriandxPipelineStack extends Stack {
             validation_lambda_stage
         )
 
-        // Add the token refresh tage to the pipeline wave
-        const token_refresh_lambda_stage = new CttsoIcaToPieriandxTokenRefreshLambdaStage(this, props.stack_prefix + "-TokenRefreshLambdaStage", {
-            stack_prefix: `${props.stack_prefix}-token-refresh-lambda-stack`,
-            env: {
-                account: props.aws_account_id,
-                region: props.aws_region
-            },
-            stack_suffix: props.stack_suffix
-        })
-
-        // Add the token_refresh lambda stage to the pipeline wave
-        pipeline_lambdas_wave.addStage(
-            token_refresh_lambda_stage
-        )
-
         // Add the launch all available payloads and update cttso lims sheet as a new pipeline wave
         // Create wave for lambda stacks
         // Due to metadata restrictions in dev, this lims is a prod-only component
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-redcap-lambda-stack.ts b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-redcap-lambda-stack.ts
index a3d4d6b..ff694b7 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-redcap-lambda-stack.ts
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-redcap-lambda-stack.ts
@@ -2,7 +2,7 @@ import {
     CfnOutput, Stack, StackProps, Duration
 } from 'aws-cdk-lib'
 import { Construct } from 'constructs';
-import { DockerImageFunction, DockerImageCode } from "aws-cdk-lib/aws-lambda";
+import { DockerImageFunction, DockerImageCode, Function as LambdaFunction } from "aws-cdk-lib/aws-lambda";
 import { StringParameter } from "aws-cdk-lib/aws-ssm";
 import { Role, ManagedPolicy, ServicePrincipal, PolicyStatement } from "aws-cdk-lib/aws-iam";
 import { Secret } from "aws-cdk-lib/aws-secretsmanager";
@@ -11,7 +11,7 @@ import {
     REDCAP_LAMBDA_FUNCTION_SSM_KEY,
     SECRETS_MANAGER_PIERIANDX_PATH, SSM_LAMBDA_FUNCTION_ARN_VALUE,
     SSM_PIERIANDX_PATH,
-    SSM_CLINICAL_LAMBDA_FUNCTION_ARN_VALUE
+    SSM_CLINICAL_LAMBDA_FUNCTION_ARN_VALUE, PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME
 } from "../constants";
 
 
@@ -210,6 +210,15 @@ export class CttsoIcaToPieriandxRedcapLambdaStack extends Stack {
             })
         )
 
+        // Step 4: Give access to the lambda function to get the pieriandx auth token
+        // Allow secret collection
+        const pieriandx_access_token_lambda_obj = LambdaFunction.fromFunctionName(
+            this,
+            'pieriandx-access-token-lambda',
+            PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME
+        )
+        pieriandx_access_token_lambda_obj.grantInvoke(<Role>lambda_function.role)
+
         // Create the ssm parameter to represent the cttso lambda function
         const ssm_parameter = new StringParameter(
             this,
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-token-refresher-lambda-stack.ts b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-token-refresher-lambda-stack.ts
deleted file mode 100644
index da24e7a..0000000
--- a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-token-refresher-lambda-stack.ts
+++ /dev/null
@@ -1,158 +0,0 @@
-import {
-    CfnOutput, Stack, StackProps, Duration
-} from 'aws-cdk-lib'
-import { Construct } from 'constructs';
-import { DockerImageFunction, DockerImageCode } from "aws-cdk-lib/aws-lambda";
-import { StringParameter } from "aws-cdk-lib/aws-ssm";
-import { Role, ManagedPolicy, ServicePrincipal, PolicyStatement } from "aws-cdk-lib/aws-iam";
-import { Secret } from "aws-cdk-lib/aws-secretsmanager";
-import { Rule, Schedule } from "aws-cdk-lib/aws-events";
-import { LambdaFunction as LambdaFunctionTarget } from "aws-cdk-lib/aws-events-targets"
-import {
-    SSM_TOKEN_REFRESH_LAMBDA_FUNCTION_ARN_VALUE,
-    SECRETS_MANAGER_PIERIANDX_PATH,
-    SSM_PIERIANDX_PATH,
-} from "../constants";
-
-
-interface CttsoIcaToPieriandxTokenRefreshLambdaStackProps extends StackProps {
-    stack_prefix: string
-    env: {
-        account: string
-        region: string
-    }
-}
-
-export class CttsoIcaToPieriandxTokenRefreshLambdaStack extends Stack {
-
-    public readonly tokenRefreshLambdaFunctionArnOutput: CfnOutput
-    public readonly tokenRefreshLambdaFunctionSSMParameterOutput: CfnOutput
-
-    constructor(scope: Construct, id: string, props: CttsoIcaToPieriandxTokenRefreshLambdaStackProps) {
-        super(scope, id, props)
-
-        // Pull out env parameters from property
-        const env = props.env
-
-        // Create role
-        const lambda_role = new Role(this,
-            `${props.stack_prefix}-LambdaExecutionRole`,
-            {
-                assumedBy: new ServicePrincipal("lambda.amazonaws.com"),
-                roleName: props.stack_prefix + "-lr",
-                managedPolicies: [
-                    ManagedPolicy.fromAwsManagedPolicyName(
-                        'service-role/AWSLambdaBasicExecutionRole'
-                    ),
-                    ManagedPolicy.fromAwsManagedPolicyName(
-                        'service-role/AWSLambdaVPCAccessExecutionRole'
-                    )
-                ]
-            }
-        )
-
-        // Create DockerImage-based lambda Function
-        const lambda_function = new DockerImageFunction(
-            this,
-            props.stack_prefix + "-LF", {
-                functionName: props.stack_prefix + "-lf",
-                description: "Token Refresher every thirty minutes!",
-                code: DockerImageCode.fromImageAsset(
-                    "./lambdas/token_refresher",
-                ),
-                role: lambda_role,
-                timeout: Duration.seconds(300)
-            }
-        )
-
-         // Create a schedule for the lambda
-        const lambda_schedule_rule = new Rule(
-            this,
-            props.stack_prefix + "-lf-trig",
-            {
-                schedule: Schedule.expression("rate(5 minutes)")
-            }
-        )
-
-        // Add target for lambda schedule
-        lambda_schedule_rule.addTarget(
-            new LambdaFunctionTarget(
-                lambda_function
-            )
-        )
-
-        // Add pieriandx ssm access to lambda policy
-        const pieriandx_vars_ssm_access_arn_as_array = [
-            "arn", "aws", "ssm",
-            env.region, env.account,
-            "parameter" + SSM_PIERIANDX_PATH + "/*"
-        ]
-
-        lambda_function.addToRolePolicy(
-            new PolicyStatement({
-                    actions: [
-                        "ssm:GetParameter"
-                    ],
-                    resources: [
-                        pieriandx_vars_ssm_access_arn_as_array.join(":")
-                    ]
-                }
-            )
-        )
-
-        // Add pieriandx secrets access to lambda policy
-        const pieriandx_secrets_path = Secret.fromSecretNameV2(
-            this,
-            `${props.stack_prefix}-pieriandx-user-password-arn`,
-            SECRETS_MANAGER_PIERIANDX_PATH
-        ).secretArn
-
-        lambda_function.addToRolePolicy(
-            new PolicyStatement({
-                    actions: [
-                        "secretsmanager:ListSecrets",
-                    ],
-                    resources: [
-                        "*"
-                    ]
-                }
-            )
-        )
-
-        lambda_function.addToRolePolicy(
-            new PolicyStatement({
-                    actions: [
-                        "secretsmanager:DescribeSecret",
-                        "secretsmanager:GetSecretValue",
-                        "secretsmanager:CreateSecret",
-                        "secretsmanager:UpdateSecret"
-                    ],
-                    resources: [
-                        `${pieriandx_secrets_path}/*`
-                    ]
-                }
-            )
-        )
-
-        // Create the ssm parameter to represent the cttso lambda function
-        const ssm_parameter = new StringParameter(
-            this,
-            props.stack_prefix + "ssm-cdk-lambda-parameter",
-            {
-                stringValue: lambda_function.functionArn,
-                parameterName: SSM_TOKEN_REFRESH_LAMBDA_FUNCTION_ARN_VALUE,
-            }
-        )
-
-        // Assign values to cfn outputs
-        this.tokenRefreshLambdaFunctionArnOutput = new CfnOutput(this, "tokenRefreshLambdaFunctionArn", {
-            value: lambda_function.functionArn,
-        });
-
-        // Add ssm parameter
-        this.tokenRefreshLambdaFunctionSSMParameterOutput = new CfnOutput(this, "tokenRefreshLambdaFunctionSSMParameterArn", {
-            value: ssm_parameter.parameterArn,
-        });
-    }
-
-}
\ No newline at end of file
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-token-refresher-lambda-stage.ts b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-token-refresher-lambda-stage.ts
deleted file mode 100644
index ce8af0d..0000000
--- a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-token-refresher-lambda-stage.ts
+++ /dev/null
@@ -1,34 +0,0 @@
-import {CfnOutput, StackProps, Stage, Tags} from "aws-cdk-lib";
-import { Construct } from "constructs";
-import { CttsoIcaToPieriandxTokenRefreshLambdaStack } from "./cttso-ica-to-pieriandx-token-refresher-lambda-stack"
-
-
-interface CttsoIcaToPieriandxTokenRefreshLambdaStageProps extends StackProps {
-    stack_prefix: string
-    env: {
-        account: string
-        region: string
-    }
-    stack_suffix: string
-}
-
-export class CttsoIcaToPieriandxTokenRefreshLambdaStage extends Stage {
-
-    public readonly tokenRefreshLambdaFunctionArnOutput: CfnOutput
-    public readonly tokenRefreshLambdaFunctionSSMParameterOutput: CfnOutput
-
-    constructor(
-        scope: Construct,
-        id: string,
-        props: CttsoIcaToPieriandxTokenRefreshLambdaStageProps
-    ) {
-        super(scope, id, props);
-
-        const lambda_batch_stack = new CttsoIcaToPieriandxTokenRefreshLambdaStack(this, props.stack_prefix, props);
-
-        Tags.of(lambda_batch_stack).add("Stack", props.stack_prefix);
-
-        this.tokenRefreshLambdaFunctionArnOutput = lambda_batch_stack.tokenRefreshLambdaFunctionArnOutput
-        this.tokenRefreshLambdaFunctionSSMParameterOutput = lambda_batch_stack.tokenRefreshLambdaFunctionSSMParameterOutput
-    }
-}
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-validation-lambda-stack.ts b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-validation-lambda-stack.ts
index 51da67e..91762fa 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-validation-lambda-stack.ts
+++ b/deploy/cttso-ica-to-pieriandx-cdk/lib/cttso-ica-to-pieriandx-validation-lambda-stack.ts
@@ -2,7 +2,7 @@ import {
     CfnOutput, Stack, StackProps, Duration
 } from 'aws-cdk-lib'
 import { Construct } from 'constructs';
-import { DockerImageFunction, DockerImageCode } from "aws-cdk-lib/aws-lambda";
+import { DockerImageFunction, DockerImageCode, Function as LambdaFunction } from "aws-cdk-lib/aws-lambda";
 import { StringParameter } from "aws-cdk-lib/aws-ssm";
 import { Role, ManagedPolicy, ServicePrincipal, PolicyStatement } from "aws-cdk-lib/aws-iam";
 import { Secret } from "aws-cdk-lib/aws-secretsmanager";
@@ -10,7 +10,7 @@ import {
     DATA_PORTAL_API_ID_SSM_PARAMETER, DATA_PORTAL_API_DOMAIN_NAME_SSM_PARAMETER,
     SSM_VALIDATION_LAMBDA_FUNCTION_ARN_VALUE,
     SECRETS_MANAGER_PIERIANDX_PATH, SSM_LAMBDA_FUNCTION_ARN_VALUE,
-    SSM_PIERIANDX_PATH,
+    SSM_PIERIANDX_PATH, PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME,
 } from "../constants";
 
 
@@ -177,6 +177,15 @@ export class CttsoIcaToPieriandxValidationLambdaStack extends Stack {
             })
         )
 
+        // Step 4: Give access to the lambda function to get the pieriandx auth token
+        // Allow secret collection
+        const pieriandx_access_token_lambda_obj = LambdaFunction.fromFunctionName(
+            this,
+            'pieriandx-access-token-lambda',
+            PIERIANDX_AUTH_TOKEN_COLLECTOR_LAMBDA_FUNCTION_NAME
+        )
+        pieriandx_access_token_lambda_obj.grantInvoke(<Role>lambda_function.role)
+
         // Create the ssm parameter to represent the cttso lambda function
         const ssm_parameter = new StringParameter(
             this,
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/project-name-to-pieriandx-mapping.json b/deploy/cttso-ica-to-pieriandx-cdk/project-name-to-pieriandx-mapping.json
index 5f7200b..b5f9832 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/project-name-to-pieriandx-mapping.json
+++ b/deploy/cttso-ica-to-pieriandx-cdk/project-name-to-pieriandx-mapping.json
@@ -79,6 +79,14 @@
     "is_identified": "identified",
     "default_snomed_term": null
   },
+  {
+    "project_owner": "KSmith",
+    "project_name": "iPredict2",
+    "panel": "subpanel",
+    "sample_type": "patient_care_sample",
+    "is_identified": "identified",
+    "default_snomed_term":null
+  },
   {
     "project_owner": "*",
     "project_name": "*",
diff --git a/deploy/cttso-ica-to-pieriandx-cdk/scripts/initialise_lims.py b/deploy/cttso-ica-to-pieriandx-cdk/scripts/initialise_lims.py
index a115c52..77f3c49 100644
--- a/deploy/cttso-ica-to-pieriandx-cdk/scripts/initialise_lims.py
+++ b/deploy/cttso-ica-to-pieriandx-cdk/scripts/initialise_lims.py
@@ -26,6 +26,7 @@
     "glims_needs_redcap",
     "redcap_sample_type",
     "redcap_is_complete",
+    "portal_run_id",
     "portal_wfr_id",
     "portal_wfr_end",
     "portal_wfr_status",