├── README.md └── docs ├── source ├── faq.rst ├── introduction.rst ├── images │ └── emerge-logo.png ├── index.rst └── conf.py ├── Makefile └── make.bat /README.md: -------------------------------------------------------------------------------- 1 | # fhir-spec 2 | eMERGE FHIR Specification 3 | -------------------------------------------------------------------------------- /docs/source/faq.rst: -------------------------------------------------------------------------------- 1 | FAQ 2 | === 3 | 4 | TODO FAQ content 5 | -------------------------------------------------------------------------------- /docs/source/introduction.rst: -------------------------------------------------------------------------------- 1 | Introduction 2 | ============ 3 | 4 | TODO introduction content 5 | -------------------------------------------------------------------------------- /docs/source/images/emerge-logo.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/submissions/fhir-specification/master/docs/source/images/emerge-logo.png -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- 1 | # Minimal makefile for Sphinx documentation 2 | # 3 | 4 | # You can set these variables from the command line. 5 | SPHINXOPTS = 6 | SPHINXBUILD = sphinx-build 7 | SOURCEDIR = source 8 | BUILDDIR = build 9 | 10 | # Put it first so that "make" without argument is like "make help". 11 | help: 12 | @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) 13 | 14 | .PHONY: help Makefile 15 | 16 | # Catch-all target: route all unknown targets to Sphinx using the new 17 | # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). 18 | %: Makefile 19 | @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- 1 | @ECHO OFF 2 | 3 | pushd %~dp0 4 | 5 | REM Command file for Sphinx documentation 6 | 7 | if "%SPHINXBUILD%" == "" ( 8 | set SPHINXBUILD=sphinx-build 9 | ) 10 | set SOURCEDIR=source 11 | set BUILDDIR=build 12 | 13 | if "%1" == "" goto help 14 | 15 | %SPHINXBUILD% >NUL 2>NUL 16 | if errorlevel 9009 ( 17 | echo. 18 | echo.The 'sphinx-build' command was not found. Make sure you have Sphinx 19 | echo.installed, then set the SPHINXBUILD environment variable to point 20 | echo.to the full path of the 'sphinx-build' executable. Alternatively you 21 | echo.may add the Sphinx directory to PATH. 22 | echo. 23 | echo.If you don't have Sphinx installed, grab it from 24 | echo.http://sphinx-doc.org/ 25 | exit /b 1 26 | ) 27 | 28 | %SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 29 | goto end 30 | 31 | :help 32 | %SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% 33 | 34 | :end 35 | popd 36 | -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- 1 | 2 | eMERGE HL7 FHIR Specification 3 | !!!!!!!!!!!!!!!!!!!!!!!!!!!!! 4 | 5 | The eMERGE HL7 FHIR Specification is a standard developed for the eMERGE network project. 6 | It has been built to guide the eMERGE FHIR implementation project which will apply this 7 | specification to a subset of the reports resulted from the eMERGE Sequencing Centers (SCs). 8 | This FHIR Specification attempts to follow the implementation guidelines being developed in 9 | parallel by the HL7 Clinical Genomics WG. The expectation of this effort is to significantly 10 | inform the efforts of the HL7 CG WG so as to expedite the creation of a normative standard for 11 | general practice in clinical genetic test reporting. 12 | 13 | .. toctree:: 14 | :maxdepth: 2 15 | :caption: Contents: 16 | 17 | introduction 18 | faq 19 | 20 | 21 | Indices and tables 22 | ================== 23 | 24 | * :ref:`genindex` 25 | * :ref:`modindex` 26 | * :ref:`search` 27 | -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- 1 | # -*- coding: utf-8 -*- 2 | # 3 | # Configuration file for the Sphinx documentation builder. 4 | # 5 | # This file does only contain a selection of the most common options. For a 6 | # full list see the documentation: 7 | # http://www.sphinx-doc.org/en/master/config 8 | 9 | # -- Path setup -------------------------------------------------------------- 10 | 11 | # If extensions (or modules to document with autodoc) are in another directory, 12 | # add these directories to sys.path here. If the directory is relative to the 13 | # documentation root, use os.path.abspath to make it absolute, like shown here. 14 | # 15 | # import os 16 | # import sys 17 | # sys.path.insert(0, os.path.abspath('.')) 18 | 19 | 20 | # -- Project information ----------------------------------------------------- 21 | 22 | project = u'emerge-fhir-spec' 23 | copyright = u'2019, eMERGE network' 24 | author = u'Committers' 25 | 26 | # The short X.Y version 27 | version = u'' 28 | # The full version, including alpha/beta/rc tags 29 | release = u'0.0.1' 30 | 31 | 32 | # -- General configuration --------------------------------------------------- 33 | 34 | # If your documentation needs a minimal Sphinx version, state it here. 35 | # 36 | # needs_sphinx = '1.0' 37 | 38 | # Add any Sphinx extension module names here, as strings. They can be 39 | # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom 40 | # ones. 41 | extensions = [ 42 | 'sphinx.ext.todo' 43 | ] 44 | 45 | # Add any paths that contain templates here, relative to this directory. 46 | templates_path = ['_templates'] 47 | 48 | # The suffix(es) of source filenames. 49 | # You can specify multiple suffix as a list of string: 50 | # 51 | # source_suffix = ['.rst', '.md'] 52 | source_suffix = '.rst' 53 | 54 | # The master toctree document. 55 | master_doc = 'index' 56 | 57 | # The language for content autogenerated by Sphinx. Refer to documentation 58 | # for a list of supported languages. 59 | # 60 | # This is also used if you do content translation via gettext catalogs. 61 | # Usually you set "language" from the command line for these cases. 62 | language = None 63 | 64 | # List of patterns, relative to source directory, that match files and 65 | # directories to ignore when looking for source files. 66 | # This pattern also affects html_static_path and html_extra_path. 67 | exclude_patterns = [] 68 | 69 | # The name of the Pygments (syntax highlighting) style to use. 70 | pygments_style = None 71 | 72 | # TODO directive output 73 | todo_include_todos = True 74 | 75 | 76 | # -- Options for HTML output ------------------------------------------------- 77 | 78 | # The theme to use for HTML and HTML Help pages. See the documentation for 79 | # a list of builtin themes. 80 | # 81 | html_theme = 'sphinx_rtd_theme' 82 | html_logo = 'images/emerge-logo.png' 83 | 84 | # Theme options are theme-specific and customize the look and feel of a theme 85 | # further. For a list of options available for each theme, see the 86 | # documentation. 87 | # 88 | # html_theme_options = {} 89 | 90 | # Add any paths that contain custom static files (such as style sheets) here, 91 | # relative to this directory. They are copied after the builtin static files, 92 | # so a file named "default.css" will overwrite the builtin "default.css". 93 | html_static_path = ['_static'] 94 | 95 | # Custom sidebar templates, must be a dictionary that maps document names 96 | # to template names. 97 | # 98 | # The default sidebars (for documents that don't match any pattern) are 99 | # defined by theme itself. Builtin themes are using these templates by 100 | # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', 101 | # 'searchbox.html']``. 102 | # 103 | # html_sidebars = {} 104 | #html_sidebars = { '**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html'] } 105 | 106 | # -- Options for HTMLHelp output --------------------------------------------- 107 | 108 | # Output file base name for HTML help builder. 109 | htmlhelp_basename = 'emerge-fhirdoc' 110 | 111 | 112 | # -- Options for LaTeX output ------------------------------------------------ 113 | 114 | latex_elements = { 115 | # The paper size ('letterpaper' or 'a4paper'). 116 | # 117 | # 'papersize': 'letterpaper', 118 | 119 | # The font size ('10pt', '11pt' or '12pt'). 120 | # 121 | # 'pointsize': '10pt', 122 | 123 | # Additional stuff for the LaTeX preamble. 124 | # 125 | # 'preamble': '', 126 | 127 | # Latex figure (float) alignment 128 | # 129 | # 'figure_align': 'htbp', 130 | } 131 | 132 | # Grouping the document tree into LaTeX files. List of tuples 133 | # (source start file, target name, title, 134 | # author, documentclass [howto, manual, or own class]). 135 | latex_documents = [ 136 | (master_doc, 'emerge-fhir.tex', u'emerge-fhir Documentation', 137 | u'Larry Babb & Mullai Murugan', 'manual'), 138 | ] 139 | 140 | 141 | # -- Options for manual page output ------------------------------------------ 142 | 143 | # One entry per manual page. List of tuples 144 | # (source start file, name, description, authors, manual section). 145 | man_pages = [ 146 | (master_doc, 'emerge-fhir', u'emerge-fhir Documentation', 147 | [author], 1) 148 | ] 149 | 150 | 151 | # -- Options for Texinfo output ---------------------------------------------- 152 | 153 | # Grouping the document tree into Texinfo files. List of tuples 154 | # (source start file, target name, title, author, 155 | # dir menu entry, description, category) 156 | texinfo_documents = [ 157 | (master_doc, 'emerge-fhir', u'emerge-fhir Documentation', 158 | author, 'emerge-fhir', 'One line description of project.', 159 | 'Miscellaneous'), 160 | ] 161 | 162 | 163 | # -- Options for Epub output ------------------------------------------------- 164 | 165 | # Bibliographic Dublin Core info. 166 | epub_title = project 167 | 168 | # The unique identifier of the text. This can be a ISBN number 169 | # or the project homepage. 170 | # 171 | # epub_identifier = '' 172 | 173 | # A unique identification for the text. 174 | # 175 | # epub_uid = '' 176 | 177 | # A list of files that should not be packed into the epub file. 178 | epub_exclude_files = ['search.html'] 179 | --------------------------------------------------------------------------------