Technical Specification for PyCCDA
This document outlines the port of BlueButton.js to Python.
Values
- Pythonic
-
The code should feel natural to a Python developer.
-
Excellent documentation
- Classes and functions should be well documented.
- Seasoned developers and new or part-time coders should all get use out of the documentation.
-
Code should be self-documenting, meaning written for readability.
-
Utilize the original BlueButton.js
- BlueButton.js serves as an implementation guide.
- Translation is easier than re-implementing. (Hopefully this is true!)
- User communities should be able to share, help, and understand each other.
Concepts
- Parser ...
- Generator ...
- Section ...
- Document ...
- Allergies
- Care Plan
- Chief Complaint
- Demographics
- Encounters
- Functional Statuses
- Immunizations
- Instructions
- Results
- Medications
- Problems
- Procedures
- Smoking Status
- Vitals
References
Todo
- Convert all BlueButton.js files from JavaScript to Python
| BlueButton.js file | Python equivalent | Notes | Ported? |
|---|---|---|---|
lib/bluebutton.js |
pyccda/__init__.py |
Not yet | |
lib/core.js |
pyccda/core/__init__.py |
Not yet | |
lib/core/codes.js |
pyccda/core/codes.py |
Not yet | |
lib/core/xml.js |
pyccda/core/xml.py |
Not yet | |
lib/documents.js |
pyccda/documents/__init__.py |
Not yet | |
lib/documents/c32.js |
pyccda/documents/c32.py |
Not yet | |
lib/documents/ccda.js |
pyccda/documents/ccda.py |
Not yet | |
lib/generators.js |
pyccda/generators/__init__.py |
Not yet | |
lib/generators/c32.js |
pyccda/generators/c32.py |
Not yet | |
lib/generators/ccda.js |
pyccda/generators/ccda.py |
Not yet | |
lib/generators/ccda_template.ejs |
N/A | ||
lib/parsers.js |
pyccda/parsers/__init__.py |
Not yet | |
lib/parsers/c32.js |
pyccda/parsers/c32/__init__.py |
Not yet | |
lib/parsers/c32/allergies.js |
pyccda/parsers/c32/allergies.py |
Not yet | |
lib/parsers/c32/demographics.js |
pyccda/parsers/c32/demographics.py |
Not yet | |
lib/parsers/c32/document.js |
pyccda/parsers/c32/document.py |
Not yet | |
lib/parsers/c32/encounters.js |
pyccda/parsers/c32/encounters.py |
Not yet | |
lib/parsers/c32/immunizations.js |
pyccda/parsers/c32/immunizations.py |
Not yet | |
lib/parsers/c32/medications.js |
pyccda/parsers/c32/medications.py |
Not yet | |
lib/parsers/c32/problems.js |
pyccda/parsers/c32/problems.py |
Not yet | |
lib/parsers/c32/procedures.js |
pyccda/parsers/c32/procedures.py |
Not yet | |
lib/parsers/c32/results.js |
pyccda/parsers/c32/results.py |
Not yet | |
lib/parsers/c32/vitals.js |
pyccda/parsers/c32/vitals.py |
Not yet | |
lib/parsers/ccda.js |
pyccda/parsers/ccd/__init__.py |
Not yet | |
lib/parsers/ccda/allergies.js |
pyccda/parsers/ccda/allergies.py |
Not yet | |
lib/parsers/ccda/care_plan.js |
pyccda/parsers/ccda/care_plan.py |
Not yet | |
lib/parsers/ccda/demographics.js |
pyccda/parsers/ccda/demographics.py |
Not yet | |
lib/parsers/ccda/document.js |
pyccda/parsers/ccda/document.py |
Not yet | |
lib/parsers/ccda/encounters.js |
pyccda/parsers/ccda/encounters.py |
Not yet | |
lib/parsers/ccda/free_text.js |
pyccda/parsers/ccda/free_text.py |
Not yet | |
lib/parsers/ccda/functional_statuses.js |
pyccda/parsers/ccda/functional_statuses.py |
Not yet | |
lib/parsers/ccda/immunizations.js |
pyccda/parsers/ccda/immunizations.py |
Not yet | |
lib/parsers/ccda/instructions.js |
pyccda/parsers/ccda/instructions.py |
Not yet | |
lib/parsers/ccda/medications.js |
pyccda/parsers/ccda/medications.py |
Not yet | |
lib/parsers/ccda/problems.js |
pyccda/parsers/ccda/problems.py |
Not yet | |
lib/parsers/ccda/procedures.js |
pyccda/parsers/ccda/procedures.py |
Not yet | |
lib/parsers/ccda/results.js |
pyccda/parsers/ccda/results.py |
Not yet | |
lib/parsers/ccda/smoking_status.js |
pyccda/parsers/ccda/smoking_status.py |
Not yet | |
lib/parsers/ccda/vitals.js |
pyccda/parsers/ccda/vitals.py |
Not yet | |
lib/renderers.js |
pyccda/renderers/__init__.py |
Not yet | |
lib/renderers/html.js |
pyccda/renderers/html.py |
Not yet |
Testing
shell$ make test
Testing serves a dual-purpose: to ensure our code works as expected and to document its intended use.
- Port original tests:
- spec/javascripts/amd_specs/bluebutton_spec.js
- spec/javascripts/amd_specs/c32_spec.js
- spec/javascripts/amd_specs/ccda_generator_spec.js
- spec/javascripts/amd_specs/ccda_spec.js
- spec/javascripts/browser_specs/bluebutton_spec.js
- spec/javascripts/browser_specs/c32_spec.js
- spec/javascripts/browser_specs/ccda_generator_spec.js
- spec/javascripts/browser_specs/ccda_spec.js
- spec/javascripts/fixtures/c32/HITSP_C32_with_HL7_IDs.xml
- spec/javascripts/fixtures/c32/HITSP_C32v2.5_Rev6_16Sections_Entries_MinimalErrors.xml
- spec/javascripts/fixtures/ccda/hl7_expected_ccda.xml
- spec/javascripts/fixtures/ccda/nist_expected_ccda.xml
- spec/javascripts/fixtures/json/allscripts_ccda_expected_output.json
- spec/javascripts/fixtures/json/c32_expected_browser_output.json
- spec/javascripts/fixtures/json/emerge_ccda_expected_output.json
- spec/javascripts/fixtures/json/hl7_ccda_expected_output.json
- spec/javascripts/fixtures/json/nist_ccda_expected_output.json
- spec/javascripts/helpers/ejs.js
- spec/javascripts/helpers/jasmine-jquery.js
- spec/javascripts/helpers/jquery.js
- spec/javascripts/helpers/shared_spec.js
- spec/javascripts/helpers/underscore.js
- spec/javascripts/node_specs/bluebutton_spec.js
- spec/javascripts/node_specs/c32_spec.js
- spec/javascripts/node_specs/ccda_generator_spec.js
-
spec/javascripts/node_specs/ccda_spec.js
-
Add additional tests to showcase Python functionality if necessary
Rationale
There are tools out there which parse and generate C-CDA, so why have another one and, furthermore, why port an existing one?
We wanted to write a C-CDA parser for use by our medical researchers and informaticians. Many of them do not have a background in computer science, but are familiar with data processing and logic.
These days, it's not difficult to search for how to do something, copy some code from a question-and-answer site, tweak a few things, and be able to, for example, pull out valuable information from one flat file format into another one that can be ingested into a database.
We have heard from these willing researchers-turned-coders who have said the existing C-CDA tools for Java have too steep of a learning curve. Also, they'd prefer to use Python since their other tools are in Python.
According to the ACM, as of July 2014, Python is the most popular language for teaching introductory computer science courses at top-ranked U.S. departments. Python is written to be easy for newcomers, but still allows coders the ability to use OOP, lambda functions, parallel programming, and much more.
Having found no active, Python libraries for C-CDA, we started to write our own. We were able to manipulate the HL7 XML Schemas to generate Python bindings from the HL7 XML Schemas using PyXB, but the resulting code was difficult to decipher. We then tried generateDS, but that failed to generate working code.
We were just about to dive into implementing the giant, 595-page specification when we found BlueButton.js. It was straigt-forward to use and we could even call it from Python and use the standard JSON module to convert the JSON into Python objects.
While that solution (XML to JSON to Python) might work for some, we wanted to completely remove the dependency on NodeJS, thus we decided to port BlueButton.js.