Merge pull request #218 from umccr/doc/update-pieriandx-troubleshooting

Update pieriandx troubleshooting list

.github/workflows/check_changelog.yml

@@ -19,11 +19,11 @@ jobs:
       # Get all file changes
       - name: Get All Changed Files
         id: get_all_changed_files
-        uses: tj-actions/changed-files@v36
+        uses: tj-actions/changed-files@v41
       # Get all changed in deploy directory
       - name: Get Deployment Changed Files
         id: get_deployment_changed_files
-        uses: tj-actions/changed-files@v36
+        uses: tj-actions/changed-files@v41
         with:
           files: deploy/*
       # List all changed files

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.

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.
@@ -359,6 +363,14 @@ 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": "*",
@@ -408,9 +420,28 @@ 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
+[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

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": "*",