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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 | ||
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# Set google secrets | ||
set_google_secrets() | ||
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# Create the new spreadsheet | ||
new_spread = Spread(spread="ctTSO LIMS", | ||
sheet="Sheet1", | ||
create_spread=True) | ||
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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" | ||
] | ||
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headers_df = pd.DataFrame(columns=new_headers) | ||
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new_spread.df_to_sheet(headers_df, headers=True, index=False, replace=True) | ||
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# Auth update | ||
# Allow users to read | ||
new_spread.add_permission( | ||
"all@umccr.org|reader" | ||
) | ||
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# Allow yourself to edit | ||
# You may need to manually add extra rows as some point | ||
new_spread.add_permission( | ||
"alexis.lucattini@umccr.org|writer" | ||
) | ||
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# Show url - to set ssm parameter | ||
print(new_spread.url) |