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Add script to download all HEAL Platform MDS (#281)
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* Added click ~= 8 to requirements.txt.

This allows us to build better command line interfaces.
Click is https://pypi.org/project/click/

* Added a basic get_heal_platform_mds_data_dicts script with CLI.

* Changed Click version to keep it in sync with other Dug requirements.

* Added overall structure.

* Added code for downloading studies.

* Completed support for downloading study identifiers.

* Added code to write out data dictionaries.

* Added support for missing dictionaries.

* Completed the integrated study/data dict download process.

* Added support for downloading data dicts not connected to studies.

* Fixed bug in downloading data dictionaries.

* Modified expected location of data dicts as per MK on Slack.

* Continued working on dbGaP export.

* First stab at data dictionary export.

* Added support for study identifiers.

* Pretty-printed XML.

* Took out debugging code.

* Expanded code for adding identifiers to the dbGaP files.

* First stab at writing out encodings.

* Cast numerical values to strings as needed by XML package.

* Added TODO to ask about the value of name.

* Fixed bugs in encoding parsing.

* Added a check to make sure the output dir doesn't exist.

* Cleaned up and improved documentation of download_from_mds().

* Documented and improved generate_dbgap_files.

* Fixed some bugs.
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gaurav authored Jul 11, 2023
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