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Tools for interacting with the API of the Treuhandstelle Greifswald

This package provides a CLI Interface and a Python Class.

Installation

Install with Pip:

pip install git+https://github.com/osaris-dev/ths-tools.git

CLI

The CLI has multiple commands:

  • test-auth: tests if the client authenticates correctly to the THS Server
  • map-psn-list: takes a list of PSNs and retrieves a map of these to the target PSNs
  • table-psn-mapper: takes a table and maps a source PSN column to a target PSN column

The --bal-user and --bal-pass options are optional, they are only required if authentication is done via Basic Auth.

Basic usage:

ths-tools -v \
    --ths-host test.ths.dzhk.med.uni-greifswald.de \
    --ssl-cert ths-test.crt --ssl-key ths-test.key \
    --bal-user my_user_name --bal-pass my_password_123 \
    --ths-api-key accounting.test.abc123 \
    --session-user-id test \
    --session-user-name test \
    --session-user-title "" \
    --session-user-firstname test \
    --session-user-lastname test \
    --session-user-role test \
    --token-study-id noStudy \
    --token-study_name noStudy \
    --token-event acc_temp_merge \
    --token-reason acc_temp_merge \
    --token-target_type accounting \
    --patient-identifier-domain temp \
    --no-accept-missing-target-id \
    map-psn-list --in-file Downloads/test-transfer-ids-20220919.txt --in-file-type text --out-file-type text

You can also put the arguments in environment variables, for example with a bash shell you can do:

export THS_HOST=test.ths.dzhk.med.uni-greifswald.de
export THS_API_KEY=accounting.test.abc123
export THS_SSL_CERT=ths-test.crt
export THS_SSL_KEY=ths-test.key
#export THS_BAL_USER=my_user_name
#export THS_BAL_PASS=my_password_123
export THS_SESSION_USER_ID=test
export THS_SESSION_USER_NAME=test
export THS_SESSION_USER_TITLE=""
export THS_SESSION_USER_FIRSTNAME=test
export THS_SESSION_USER_LASTNAME=test
export THS_SESSION_USER_ROLE=test
export THS_TOKEN_STUDY_ID=noStudy
export THS_TOKEN_STUDY_NAME=noStudy
export THS_TOKEN_EVENT=acc_temp_merge
export THS_TOKEN_REASON=acc_temp_merge
export THS_TOKEN_TARGET_TYPE=accounting
export THS_PATIENT_IDENTIFIER_DOMAIN=temp

ths-tools -v map-psn-list --in-file Downloads/test-transfer-ids-20220919.txt --in-file-type text --out-file-type text

The table-psn-mapper takes a table as input and output and maps a specified source column to a target column.

Usage: ths-tools table-psn-mapper [OPTIONS]

Options:
  --in-file PATH                  input file with PSNs
  --in-file-type [json|csv|xlsx]  input file type
  --in-file-json-orient TEXT      input file json structure (pandas orient
                                  flag)

  --in-file-csv-encoding TEXT     input file type
  --in-file-csv-sep TEXT          input file CSV seperator
  --out-file PATH                 output file with mapping
  --out-file-type [json|csv|xlsx]
                                  output file type
  --out-file-json-orient TEXT     output file json structure (pandas orient
                                  flag)

  --out-file-csv-encoding TEXT    output file type
  --out-file-csv-sep TEXT         output file CSV seperator
  --source-psn-column TEXT        column with PSNs to map
  --target-psn-column TEXT        new column with mapped PSNs
  --drop-source-psn-column / --no-drop-source-psn-column
                                  drop column with PSNs to map (if they are
                                  not identical)

  --help                          Show this message and exit.

Example:

ths-tools -v table-psn-mapper --in-file test.csv --in-file-type csv --out-file test-mapped.csv --out-file-type csv --source-psn-column source_psn --target-psn-column target_psn

Use the Python Class

After installing the Package with Pip you can use the THS class. See example.py.

Development

Release new version

NEW_VERSION=0.x.y
git checkout main && git merge dev && git tag $NEW_VERSION; git push origin; git push origin --tags; git push github; git push github --tags; git checkout dev; git push origin; git push github