edc-pdutils
Use pandas with the Edc
Using the management command to export to CSV and STATA
The export_models management command requires you to log in with an account that has export permissions.
The basic command requires an app_label (-a) and a path to the export folder (-p)
By default, the export format is CSV but delimited using the pipe delimiter, |.
Export one or more modules
python manage.py export_models -a ambition_subject -p /ambition/exportThe -a excepts more than one app_label
python manage.py export_models -a ambition_subject,ambition_prn,ambition_ae -p /ambition/exportExport data in CSV format or STATA format
To export as CSV where the delimiter is |
python manage.py export_models -a ambition_subject -p /ambition/exportTo export as STATA dta use option -f stata
python manage.py export_models -a ambition_subject -p /ambition/export -f stataExport encrypted data
To export encrypted fields include option --decrypt:
python manage.py export_models -a ambition_subject -p /ambition/export --decryptNote: If using the --decrypt option, the user account will need PII_EXPORT permissions
Export with a simple file name
To export using a simpler filename that drops the tablename app_label prefix and does not include a datestamp suffix.
Add option --use_simple_filename.
python manage.py export_models -a ambition_subject -p /ambition/export --use_simple_filenameExport for a country only
Add option --country.
python manage.py export_models -a ambition_subject -p /ambition/export --country="uganda"Export manually
To export Crf data, for example:
from edc_pdutils.df_exporters import CsvCrfTablesExporter
from edc_pdutils.df_handlers import CrfDfHandler
app_label = 'ambition_subject'
csv_path = '/Users/erikvw/Documents/ambition/export/'
date_format = '%Y-%m-%d'
sep = '|'
exclude_history_tables = True
class MyDfHandler(CrfDfHandler):
visit_tbl = f'{app_label}_subjectvisit'
exclude_columns = ['form_as_json', 'survival_status','last_alive_date',
'screening_age_in_years', 'registration_datetime',
'subject_type']
class MyCsvCrfTablesExporter(CsvCrfTablesExporter):
visit_column = 'subject_visit_id'
datetime_fields = ['randomization_datetime']
df_handler_cls = MyDfHandler
app_label = app_label
export_folder = csv_path
sys.stdout.write('\n')
exporter = MyCsvCrfTablesExporter(
export_folder=csv_path,
exclude_history_tables=exclude_history_tables
)
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'
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)Settings
EXPORT_FILENAME_TIMESTAMP_FORMAT: True/False (Default: False)
By default a timestamp of the current date is added as a suffix to CSV export filenames.
By default a timestamp of format %Y%m%d%H%M%S is added.
EXPORT_FILENAME_TIMESTAMP_FORMAT may be set to an empty string or a valid format for strftime.
If EXPORT_FILENAME_TIMESTAMP_FORMAT is set to an empty string, “”, a suffix is not added.
For example:
# default
registered_subject_20190203112555.csv
# EXPORT_FILENAME_TIMESTAMP_FORMAT = "%Y%m%d"
registered_subject_20190203.csv
# EXPORT_FILENAME_TIMESTAMP_FORMAT = ""
registered_subject.csv2 maintainers
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