Merge pull request #209 from umccr/dev

Ensure gspread is less than version 6.0.0

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.  
 
+## 2024-02-02
+
+> Author: Alexis Lucattini
+> Email: [[email protected]](mailto:[email protected])
+
+### Dependencies
+* Ensure gspread is less than version 6.0.0 (https://github.com/umccr/cttso-ica-to-pieriandx/pull/208)
+
+
 ## 2023-11-27
 
 > Author: Alexis Lucattini

deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/requirements.txt

@@ -2,6 +2,7 @@ aws_requests_auth==0.4.3
 boto3==1.26.68
 botocore==1.29.68
 gspread_pandas==3.2.2
+gspread<6.0.0
 mypy_boto3_lambda==1.26.55
 mypy_boto3_secretsmanager==1.26.49
 mypy_boto3_ssm==1.26.43

deploy/cttso-ica-to-pieriandx-cdk/scripts/initialise_lims.py

@@ -0,0 +1,66 @@
+from lambda_utils.gspread_helpers import set_google_secrets
+from gspread_pandas import Spread
+import pandas as pd
+
+# Set google secrets
+set_google_secrets()
+
+# Create the new spreadsheet
+new_spread = Spread(spread="ctTSO LIMS",
+                    sheet="Sheet1",
+                    create_spread=True)
+
+new_headers = [
+    "subject_id",
+    "library_id",
+    "in_glims",
+    "in_portal",
+    "in_redcap",
+    "in_pieriandx",
+    "glims_project_owner",
+    "glims_project_name",
+    "glims_panel",
+    "glims_sample_type",
+    "glims_is_identified",
+    "glims_default_snomed_term",
+    "glims_needs_redcap",
+    "redcap_sample_type",
+    "redcap_is_complete",
+    "portal_wfr_id",
+    "portal_wfr_end",
+    "portal_wfr_status",
+    "portal_sequence_run_name",
+    "portal_is_failed_run",
+    "pieriandx_submission_time",
+    "pieriandx_case_id",
+    "pieriandx_case_accession_number",
+    "pieriandx_case_creation_date",
+    "pieriandx_case_identified",
+    "pieriandx_assignee",
+    "pieriandx_disease_code",
+    "pieriandx_disease_label",
+    "pieriandx_panel_type",
+    "pieriandx_sample_type",
+    "pieriandx_workflow_id",
+    "pieriandx_workflow_status",
+    "pieriandx_report_status"
+]
+
+headers_df = pd.DataFrame(columns=new_headers)
+
+new_spread.df_to_sheet(headers_df, headers=True, index=False, replace=True)
+
+# Auth update
+# Allow users to read
+new_spread.add_permission(
+    "[email protected]|reader"
+)
+
+# Allow yourself to edit
+# You may need to manually add extra rows as some point
+new_spread.add_permission(
+    "[email protected]|writer"
+)
+
+# Show url - to set ssm parameter
+print(new_spread.url)