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Merge remote-tracking branch 'origin/dev' into dev
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alexiswl committed Feb 2, 2024
2 parents 1045da9 + a1f7017 commit 962d813
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Expand Up @@ -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
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66 changes: 66 additions & 0 deletions deploy/cttso-ica-to-pieriandx-cdk/scripts/initialise_lims.py
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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)

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