Use pandas with clinicedc/edc projects
Project description
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'
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'
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.csv
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