castoredc-api 0.1.9.1

Python wrapper for the Castor EDC API

CastorEDC API

Features

Supports CastorEDC Release 2023.2

This is a Python package for interacting with the API of Castor Electronic Data Capture (EDC). The package contains functions to interact with all the endpoints defined on https://data.castoredc.com/api#/. Within the package are functions for easy export and import of your data through the API.

Export

Supported export formats are

• Pandas
• CSV
• R (using Feather)

Import

Import currently only supports .xlsx files with some configuration.
See for more information below.

Getting Started

1. Install the package
   • pip install castoredc-api
   • conda install -c conda-forge castoredc_api
   • conda install -c reiniervl castoredc_api
2. Import the client
3. Instantiate the client with your client-ID and client-secret (don't share these!) and url to the server.
   • ID and secret: Account -> Settings -> Castor EDC API
   • url: region.castoredc.com
4. Link the client to your study with the study-ID
   • ID: Study -> Settings -> Castor Study ID
5. Use the wrapper functions to start working with your study.

For all implemented functions, see: https://data.castoredc.com/api#/

from castoredc_api import CastorClient

# Create a client with your credentials
c = CastorClient('MYCLIENTID', 
                 'MYCLIENTSECRET', 
                 'data.castoredc.com')

# Link the client to your study in the Castor EDC database
c.link_study('MYSTUDYID')

# Then you can interact with the API
# Get all records
c.all_records()

# Create a new survey package
c.create_survey_package_instance(survey_package_id="FAKESURVEY-PACKAGE-ID",
                                 record_id="TEST-RECORD",
                                 email_address="[e-mail]",
                                 auto_send=True)

Export

1. Instantiate the CastorStudy with your credentials, study ID and server url.
2. Use the Study functions to start working with your database

For exporting data: The endpoint that extracts data for the study can't be used if the authenticated user has a role within the study.
See: https://data.castoredc.com/api#/export/get_study__study_id__export_data

from castoredc_api import CastorStudy

# Instantiate Study
study = CastorStudy('MYCLIENTID', 
                    'MYCLIENTSECRET', 
                    'MYSTUDYID', 
                    'data.castoredc.com')

# Export your study to pandas dataframes or CSV files
study.export_to_dataframe()
study.export_to_csv()

# Data and structure mapping are automatically done on export, but you can also map these without exporting your data
# Map your study data locally (also maps structure)
study.map_data()

# Map only your study structure locally
study.map_structure()

# After mapping data and/or structure, you can start working with your study
# Get all reports
study.get_all_report_forms()
# Get all data points of a single record
study.get_single_record('000011').get_all_data_points()

Data Formatting

Date fields are returned as strings (dd-mm-yyyy)
Datetime fields are returned as strings (dd-mm-yyyy hh-mm)
Numeric fields are all returned as floats.

This can be changed by supplying the argument format_options when intialising the CastorStudy.
Allowed options are date, datetime, datetime_seconds and time.
See https://docs.python.org/3/library/datetime.html#strftime-strptime-behavior for formatting options.

from castoredc_api import CastorStudy

# Instantiate Study with different formatting settings
study = CastorStudy('MYCLIENTID', 
                    'MYCLIENTSECRET', 
                    'MYSTUDYID', 
                    'data.castoredc.com', 
                    format_options={
                      "date": "%B %e %Y",
                      "datetime": "%B %e %Y %I:%M %p",
                      "datetime_seconds": "%B %e %Y %I:%M:%S %p",
                      "time": "%I:%M %p",
                    })

Missing Data

Missing data is mostly handled through pandas (NaN).

User-defined missing data is handled through its definitions in Castor.
For numeric and text-like variables, these values are -95, -96, -97, -98 and -99.
For datetime data, missing data values are with the years 2995, 2996, 2997, 2998, and 2999.

Import

1. Instantiate the CastorStudy with your credentials, study ID and server url.
2. Format your data in the right format (see below)
3. Create a link file to link external and Castor variables (see below)
4. (Optional) Create a variable translation file to translate values and labels to Castor optiongroups (see below).
5. (Optional) Create a merge file to merge multiple columns into one CastorField (see below).
6. (Optional) Set date, datetime and time formatting to translate local format into Castor format (see below).
7. Import your data with the import_data function.
   • If label_data is set to true, it translates the string values to their integer values of the optiongroup in Castor.
   • If set to false, it takes the integer values as is.

Data is validated against the Castor database, meaning that:

• Existence of records and fields is checked
• Numeric values are compared against allowed values (min & max)
• Date(time) and time formats are compared against the specified format

Synchronous Upload

The synchronous upload option uploads each row one by one.
When an Error is encountered or the upload finishes successfully, the program outputs the upload log to the output folder and stops.

Asynchronous Upload

The asynchronous upload option uploads each row one by one.
This is about 15-30 times faster than synchronous upload.
The program does not stop if uploading a row encounters an error.
When the upload finishes, the program outputs the upload log to the output folder and stops.
Error messages are stored in the output folder for debugging.

Simple Example

from castoredc_api import CastorStudy
from castoredc_api import import_data

# Create a Study with your credentials
study = CastorStudy('MYCLIENTID',
                    'MYCLIENTSECRET',
                    'MYSTUDYID',
                    'data.castoredc.com')

# Import labelled study data
imported_data = import_data(data_source_path="PATH/TO/YOUR/LABELLED/STUDY/DATA",
                            column_link_path="PATH/TO/YOUR/LINK/FILE", 
                            study=study, 
                            label_data=True, 
                            target="Study")

# Import labelled study data (asynchronous)
imported_data = import_data(data_source_path="PATH/TO/YOUR/LABELLED/STUDY/DATA",
                            column_link_path="PATH/TO/YOUR/LINK/FILE", 
                            study=study, 
                            label_data=True, 
                            target="Study",
                            use_async=True)

# Import non-labelled report data
imported_data = import_data(data_source_path="PATH/TO/YOUR/REPORT/DATA", 
                            column_link_path="PATH/TO/YOUR/LINK/FILE",
                            study=study, 
                            label_data=False, 
                            target="Report", 
                            target_name="Medication")

# Import labelled survey data
imported_data = import_data(data_source_path="PATH/TO/YOUR/LABELLED/SURVEY/DATA",
                            column_link_path="PATH/TO/YOUR/LINK/FILE", 
                            study=study, 
                            label_data=True, 
                            target="Survey",
                            target_name="My first survey package", 
                            email="[e-mail]")

Specifying the data structure

Data files

See below and example_files/ for an examples.

• Dates should be formatted as dd-mm-yyyy.
• Datetime should be formatted as dd-mm-yyyy;hh:mm
• Use semicolons for fields that allow multiple options (e.g. checkboxes)
• If any value for a column is translated, all values should have a translation mapped (see below)

Labels

The mg/4 weeks and mg/8 weeks under units will be imported to the med_other_unit fields as they do not match any option of the optiongroup, see link files.

Example

patient	medication	startdate	stopdate	dose	units
110001	Azathioprine	05-12-2019	05-12-2020	0.05	g/day
110002	Vedolizumab	17-08-2018	17-09-2020	300	mg/4 weeks
110003	Ustekinumab	19-12-2017	03-06-2019	90	mg/8 weeks
110004	Thioguanine	25-04-2020	27-05-2021	15	mg/day
110005	Tofacitinib	01-03-2020	31-12-2999	10	mg/day

Values

The non-integer variables under units will be imported to the med_other_unit fields as they do not match any optionvalue of the optiongroup, see link files.

Example

patient	medication	startdate	stopdate	dose	units
110001	Azathioprine	05-12-2019	05-12-2020	0.05	3
110002	Vedolizumab	17-08-2018	17-09-2020	300	mg/4 weeks
110003	Ustekinumab	19-12-2017	03-06-2019	90	mg/8 weeks
110004	Thioguanine	25-04-2020	27-05-2021	15	2
110005	Tofacitinib	01-03-2020	31-12-2999	10	2

Link files

Link files should be of the format as shown below. The mapping is variable name in the Excel file -> variable name in Castor. If a variable in other is referenced twice in the Castor column, it means that it has a dependency in Castor.

This is a way to import data that has an "other" category, for example a radio question that reads:

• A
• B
• C
• Other

In which case selecting other opens a new text box to enter this information. The second variable in the link_file should be this new text box.

This is treated in the following manner:

• First, the data is mapped to the first variable referenced
• For all data that could not be mapped to the first variable, the 'other' category is selected in the first variable
• Then the data that could not be mapped is written to the second variable referenced.

Example

other	castor
patient	record_id
medication	med_name
startdate	med_start
stopdate	med_stop
dose	med_dose
units	med_units
units	med_other_unit

Translation files

Translation files link the optiongroup value or label from the external database to the optiongroups from Castor. Values are translated for all variables specified in the first column of the file.

Two situations can occur when a value is encountered for which no translation is given:

• If a dependent field is specified (see link files): the value is not translated and imported to the dependent field.
• If no dependent field is specified: the program gives an error. In this situation, every value that occurs in the external database needs to be mapped.

Example

variable	other	castor
family disease history	none	None
family disease history	don't know	Unknown
family disease history	deaf	Deafness
family disease history	cardiomyopathy	(Cardio)myopathy
family disease history	encephalopathy	Encephalopathy
family disease history	diabetes	Diabetes Mellitus
family disease history	cardiovascular disease	Hypertension/Cardiovascular disease
family disease history	thromboembolism	Thrombosis
family disease history	tumor	Malignancy

from castoredc_api import CastorStudy
from castoredc_api import import_data

# Create a Study with your credentials
study = CastorStudy('MYCLIENTID',
                    'MYCLIENTSECRET',
                    'MYSTUDYID',
                    'data.castoredc.com')

# Import study data with a translation file
imported_data = import_data(data_source_path="PATH/TO/YOUR/LABELLED/STUDY/DATA",
                            column_link_path="PATH/TO/YOUR/LINK/FILE", 
                            study=study, 
                            label_data=True, 
                            target="Study",
                            translation_path="PATH/TO/YOUR/TRANSLATION/FILE")

Merge files

Merge files link the multiple columns from the external database to a single checkbox field in Castor.
For each column from the external database specified under other_variable the value under other_value is mapped to the castor_value for the castor_variable.
If specifying a merge file, note that castor_value is the new other variable for your link file (see below).
All other_values not defined raise an Error. Only supports many-to-one matching.

Example

Data File

patient	date baseline blood sample	baseline hemoglobin	factor V Leiden	datetime onset stroke	time onset trombectomy	year of birth	patient sex	patient race	famhist_none	famhist_deaf	famhist_cardiomyopathy	famhist_encephalopathy	famhist_diabmell	famhist_cardiovasc	famhist_malignancy	famhist_unknown
110001	16-03-2021	8.3	55;16-03-2021	16-03-2021;07:30	09:25	1999	Female	Asian	No	No	Yes	Yes	Yes	No	No	No
110002	17-03-2021	7.2	33;17-03-2021	17-03-2021;15:30	06:33	1956	Female	African/black	No	Yes	Yes	No	No	No	No	No
110003	16-03-2022	9.1	-45;18-03-2022	18-03-2022;02:00	12:24	1945	Male	Chinese	Yes	No	No	No	No	No	No	No
110004	17-03-2022	3.2	28;19-03-2022	17-03-2022;21:43	23:23	1933	Male	Caucasian/white	No	No	No	No	No	Yes	Yes	No
110005	16-03-2023	10.3	5;20-03-2023	16-03-2023;07:22	08:14	1921	Female	Hispanic	No	No	No	No	No	No	No	Yes

Merge File

other_variable	other_value	castor_variable	castor_value
famhist_none	Yes	his_family	None
famhist_deaf	Yes	his_family	Deafness
famhist_cardiomyopathy	Yes	his_family	(Cardio)myopathy
famhist_encephalopathy	Yes	his_family	Encephalopathy
famhist_diabmell	Yes	his_family	Diabetes Mellitus
famhist_cardiovasc	Yes	his_family	Hypertension/Cardiovascular disease
famhist_malignancy	Yes	his_family	Malignancy
famhist_unknown	Yes	his_family	Unknown
famhist_none	No	his_family
famhist_deaf	No	his_family
famhist_cardiomyopathy	No	his_family
famhist_encephalopathy	No	his_family
famhist_diabmell	No	his_family
famhist_cardiovasc	No	his_family
famhist_malignancy	No	his_family
famhist_unknown	No	his_family

Link File

other	castor
patient	record_id
date baseline blood sample	base_bl_date
baseline hemoglobin	base_hb
factor V Leiden	fac_V_leiden
datetime onset stroke	onset_stroke
time onset trombectomy	onset_trombectomy
year of birth	pat_birth_year
patient sex	pat_sex
patient race	pat_race
his_family	his_family

from castoredc_api import CastorStudy
from castoredc_api import import_data

# Create a Study with your credentials
study = CastorStudy('MYCLIENTID',
                    'MYCLIENTSECRET',
                    'MYSTUDYID',
                    'data.castoredc.com')

# Import study data with a merge file
imported_data = import_data(data_source_path="PATH/TO/YOUR/LABELLED/STUDY/DATA",
                            column_link_path="PATH/TO/YOUR/LINK/FILE", 
                            study=study, 
                            label_data=True, 
                            target="Study",
                            merge_path="PATH/TO/YOUR/MERGE/FILE")

Data Formatting

Standard date formatting settings are the following. Date(time) and time fields should follow these formats in the Excel sheet to be uploaded.

• Date = dd-mm-yyyy
• Datetime = dd-mm-yyyy;hh-mm
• Time = hh:mm
• Decimal separator = .

These can be changed by supplying the argument format_options when calling create upload.
Allowed options are date, datetime, and time. Decimal separator cannot be changed.
See https://docs.python.org/3/library/datetime.html#strftime-strptime-behavior for formatting options.

from castoredc_api import CastorStudy
from castoredc_api import import_data

# Create a Study with your credentials
study = CastorStudy('MYCLIENTID',
                    'MYCLIENTSECRET',
                    'MYSTUDYID',
                    'data.castoredc.com')

# Import labelled study data with changed formats
imported_data = import_data(data_source_path="PATH/TO/YOUR/LABELLED/STUDY/DATA",
                            column_link_path="PATH/TO/YOUR/LINK/FILE", 
                            study=study, 
                            label_data=True, 
                            target="Study",
                            format_options={
                               "date": "%B %d %Y",
                               "datetime": "%B %d %Y %I:%M %p",
                               "time": "%I:%M %p",
                            })

Prerequisites

1. Python Version >= 3.8
2. See requirements.txt

Known Issues

1. Async import and export cannot be used in an IPython environment, see this discussion
2. Feather export is uncompressed, see this issue
3. Device token and Econsent endpoints are untested. Use at your own risk.

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Running Tests

Want to contribute to the testing suite? Or test possible changes you want to contribute? Tests can be ran via two methods: on Github and on your local machine.

On Github: when you create a pull request for this project, Pytest automatically runs for the testing suite (see pytest.yml). If you have added a whole new testing module, don't forget to add this to the pytest.yml file. Within the repository, applicable access rights have been set for the client. Use the following fixtures for the respective modules you want to test:

• Testing API read endpoints: client
• Testing API write endpoints: write_client
• Testing output:
  • For structure output to Python: integration_study & integration_study_format
  • For data output to Python: integration_study_mapped & integration_study_format_mapped
  • For data output to csv: output_data
• Testing importing of data: import_study

Locally: You can only run tests locally when you have read and write access to the correct Castor Studies. Please send a message to the repository owner to ask for the correct access, with information on why. Access and correct study IDs will then be given to run the tests.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Authors

• R.C.A. van Linschoten - Initial Development - Reinier van Linschoten

See also the list of contributors who participated in this project.

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments

• Franciscus Gasthuis & Vlietland for making time available for development
• Castor EDC for support and code review