diff --git a/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md b/deploy/cttso-ica-to-pieriandx-cdk/Changelog.md index 1844b46..74a3145 100644 --- 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. +## 2024-02-02 + +> Author: Alexis Lucattini +> Email: [Alexis.Lucattini@umccr.org](mailto:alexis.lucattini@umccr.org) + +### 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 diff --git a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/requirements.txt b/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/requirements.txt index 67f4e1a..c6fde7f 100644 --- a/deploy/cttso-ica-to-pieriandx-cdk/lambdas/layers/requirements.txt +++ b/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 diff --git a/deploy/cttso-ica-to-pieriandx-cdk/scripts/initialise_lims.py b/deploy/cttso-ica-to-pieriandx-cdk/scripts/initialise_lims.py new file mode 100644 index 0000000..a115c52 --- /dev/null +++ b/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( + "all@umccr.org|reader" +) + +# Allow yourself to edit +# You may need to manually add extra rows as some point +new_spread.add_permission( + "alexis.lucattini@umccr.org|writer" +) + +# Show url - to set ssm parameter +print(new_spread.url)