edc-pdutils 0.1.3

Use pandas with clinicedc/edc projects

edc-pdutils

Use pandas with the Edc

To export Crf data, for example:

csv_path = '/Users/erikvw/Documents/ambition/export/'
date_format = '%Y-%m-%d'
sep = ','

class MyDfHandler(CrfDfHandler):
    visit_tbl = 'ambition_subject_subjectvisit'
    registered_subject_tbl = 'edc_registration_registeredsubject'
    appointment_tbl = 'edc_appointment_appointment'
    exclude_columns = ['form_as_json', 'survival_status','last_alive_date',
                       'screening_age_in_years', 'registration_datetime',
                       'subject_type']

class MyCsvCrfTablesExporter(CsvCrfTablesExporter):
    visit_columns = ['subject_visit_id']
    datetime_fields = ['randomization_datetime']
    df_handler_cls = MyDfHandler
    app_label = 'ambition_subject'
    export_folder = csv_path

sys.stdout.write('\n')
exporter = MyCsvCrfTablesExporter()
exporter.to_csv(date_format=date_format, delimiter=sep)

To export INLINE data for any CRF configured with an inline, for example:

class MyDfHandler(CrfDfHandler):
    visit_tbl = 'ambition_subject_subjectvisit'
    registered_subject_tbl = 'edc_registration_registeredsubject'
    appointment_tbl = 'edc_appointment_appointment'
    exclude_columns = ['form_as_json', 'survival_status','last_alive_date',
                       'screening_age_in_years', 'registration_datetime',
                       'subject_type']


class MyCsvCrfInlineTablesExporter(CsvCrfInlineTablesExporter):
    visit_columns = ['subject_visit_id']
    df_handler_cls = MyDfHandler
    app_label = 'ambition_subject'
    export_folder = csv_path
    exclude_inline_tables = [
        'ambition_subject_radiology_abnormal_results_reason',
        'ambition_subject_radiology_cxr_type']
sys.stdout.write('\n')
exporter = MyCsvCrfInlineTablesExporter()
exporter.to_csv(date_format=date_format, delimiter=sep)