Adding sct_dbtool, first import.

sct_dbtool/docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = sct_dbtool
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

sct_dbtool/docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+set SPHINXPROJ=sct_dbtool
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS%
+
+:end
+popd

sct_dbtool/docs/source/conf.py

@@ -0,0 +1,178 @@
+# -*- coding: utf-8 -*-
+#
+# Configuration file for the Sphinx documentation builder.
+#
+# This file does only contain a selection of the most common options. For a
+# full list see the documentation:
+# http://www.sphinx-doc.org/en/master/config
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+
+sys.path.insert(0, os.path.abspath('.'))
+
+import sct_dbtool
+
+# -- Project information -----------------------------------------------------
+
+project = 'sct_dbtool'
+copyright = '2018, Christian S. Perone'
+author = 'Christian S. Perone'
+
+# The short X.Y version
+version = sct_dbtool.__version__
+# The full version, including alpha/beta/rc tags
+release = sct_dbtool.__version__
+
+
+# -- General configuration ---------------------------------------------------
+
+# If your documentation needs a minimal Sphinx version, state it here.
+#
+# needs_sphinx = '1.0'
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.viewcode',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# The suffix(es) of source filenames.
+# You can specify multiple suffix as a list of string:
+#
+# source_suffix = ['.rst', '.md']
+source_suffix = '.rst'
+
+# The master toctree document.
+master_doc = 'index'
+
+# The language for content autogenerated by Sphinx. Refer to documentation
+# for a list of supported languages.
+#
+# This is also used if you do content translation via gettext catalogs.
+# Usually you set "language" from the command line for these cases.
+language = None
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path .
+exclude_patterns = []
+
+# The name of the Pygments (syntax highlighting) style to use.
+pygments_style = 'sphinx'
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Theme options are theme-specific and customize the look and feel of a theme
+# further.  For a list of options available for each theme, see the
+# documentation.
+#
+html_theme_options = {
+    'github_user': 'neuropoly',
+    'github_repo': 'sct_testing_management',
+    'github_button': True,
+    'github_banner': False,
+    'logo_name': True,
+}
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# Custom sidebar templates, must be a dictionary that maps document names
+# to template names.
+#
+# The default sidebars (for documents that don't match any pattern) are
+# defined by theme itself.  Builtin themes are using these templates by
+# default: ``['localtoc.html', 'relations.html', 'sourcelink.html',
+# 'searchbox.html']``.
+#
+# html_sidebars = {}
+html_sidebars = {
+    '**': [
+        'about.html',
+        'navigation.html',
+        'relations.html',
+        'searchbox.html',
+        'donate.html',
+    ]
+}
+
+html_scaled_image_link = False
+
+# -- Options for HTMLHelp output ---------------------------------------------
+
+# Output file base name for HTML help builder.
+htmlhelp_basename = 'sct_dbtooldoc'
+
+
+# -- Options for LaTeX output ------------------------------------------------
+
+latex_elements = {
+    # The paper size ('letterpaper' or 'a4paper').
+    #
+    # 'papersize': 'letterpaper',
+
+    # The font size ('10pt', '11pt' or '12pt').
+    #
+    # 'pointsize': '10pt',
+
+    # Additional stuff for the LaTeX preamble.
+    #
+    # 'preamble': '',
+
+    # Latex figure (float) alignment
+    #
+    # 'figure_align': 'htbp',
+}
+
+# Grouping the document tree into LaTeX files. List of tuples
+# (source start file, target name, title,
+#  author, documentclass [howto, manual, or own class]).
+latex_documents = [
+    (master_doc, 'sct_dbtool.tex', 'sct\\_dbtool Documentation',
+     'Christian S. Perone', 'manual'),
+]
+
+
+# -- Options for manual page output ------------------------------------------
+
+# One entry per manual page. List of tuples
+# (source start file, name, description, authors, manual section).
+man_pages = [
+    (master_doc, 'sct_dbtool', 'sct_dbtool Documentation',
+     [author], 1)
+]
+
+
+# -- Options for Texinfo output ----------------------------------------------
+
+# Grouping the document tree into Texinfo files. List of tuples
+# (source start file, target name, title, author,
+#  dir menu entry, description, category)
+texinfo_documents = [
+    (master_doc, 'sct_dbtool', 'sct_dbtool Documentation',
+     author, 'sct_dbtool', 'One line description of project.',
+     'Miscellaneous'),
+]
+
+
+# -- Extension configuration -------------------------------------------------

sct_dbtool/docs/source/getstarted.rst

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+Introduction
+==============================================================================
+This is the documentation for the command-line tool `sct_dbtool`. This tool
+will apply custom checks into each item of the MRI database.
+
+Installation
+------------------------------------------------------------------------------
+To install it, clone the repository and install with::
+
+    pip install .
+
+If you want, you can create a python environment with Anaconda::
+
+	conda create -n dbtoolenv python=3.6
+	source activate dbtoolenv
+
+Before installing it.
+
+Configuration
+------------------------------------------------------------------------------
+Before running the tool, it must be configured with the database credentials,
+in order to do that, just execute the following command below::
+
+    sct_dbtool setup
+
+And then answer the questions about the credentials for the Web Management
+system.
+
+How to use it
+------------------------------------------------------------------------------
+To use it, just run the following command::
+
+    sct_dbtool sanity ../duke/sct_testing/large
+
+Where the last parameter is the path to where the database files are. After
+running it, the tool will generate a output report called `report.html` that
+can be opened on any browser.
+
+Implementing more checks
+------------------------------------------------------------------------------
+All sanity checks are implemented in :py:mod:`sct_dbtool.sanity` module. All
+sanity checks should inherit from the class
+:py:class:`.sanity.SanityCheck`. An example is the checking
+:py:class:`.sanity.CheckEmptyDemographics` that will check
+if the demographics field is present in each item of the database,
+the code is shown below:
+
+.. code-block:: python
+
+    class CheckEmptyDemographics(SanityCheck):
+
+        def __init__(self, db_path: str):
+            super().__init__("warning", db_path)
+
+        def check(self, item: Dict):
+            if "demographic" not in item:
+                self.add_diagnostic("Demographic field not present.", item)
+                return
+
+            if item["demographic"] is None:
+                self.add_diagnostic("Demographic field is empty.", item)
+
+As you can see, the class inherits from :py:class:`.sanity.SanityCheck`
+and it implements two methods:
+
+* :py:meth:`__init__()`: this is the class constructor, you should just
+  specify the category of the check, which can be *warning*, *error* or
+  *info*. And call the base class constructor with this argument
+  and the `db_path` argument;
+
+* :py:meth:`check()`: this is the method that implements the check itself.
+  The `item` argument is a Python dictionary with the database item data.
+  In the example above, we're just checking if the "demographic" field
+  is present in this dictionary, and if not, it will call the method
+  :py:meth:`.SanityCheck.add_diagnostic()` that will add a new diagnostic
+  message for this item with a custom message.
+
+  After adding a new class, the tool will automatically use this new
+  class to check every database item in the next run of the `sct_dbtool sanity`
+  checking. It will also add this class name as filter in the report as
+  well as all diagnostic messages generated by this checking.
+
+  If you need to refer any file in the file system, as used by other checks
+  to check if the file mentioned in the database is present in the file system,
+  you can just use the :py:attr:`.SanityCheck.db_path` object attribute, that contains
+  the path of the file system that was passed as argument to the `sct_dbtool`.
+
+Please check other examples in the module :py:mod:`sct_dbtool.sanity` for more information.
+
+
+
+
+

sct_dbtool/docs/source/index.rst

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+.. sct_dbtool documentation master file, created by
+   sphinx-quickstart on Sat Jul  7 12:30:25 2018.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+SCT DB Tool documentation
+=========================================
+This is the website for the SCT DB Tool documentation. SCT DB Tool is an application
+that contains tools such as sanity checking for the MRI database.
+
+.. image:: _static/screenshot.png
+    :align: center
+    :scale: 80%
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   getstarted
+   modules
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

sct_dbtool/docs/source/modules.rst

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+API Documentation
+===============================================================================
+
+All modules above listed are under the "sct_dbtool" namespace.
+
+Contents:
+
+.. toctree::
+    :maxdepth: 4
+
+
+:mod:`sct_dbtool.api` -- Server API
+-------------------------------------------------------------------------------
+.. automodule:: sct_dbtool.api
+    :members:
+
+
+:mod:`sct_dbtool.sanity` -- Sanity Checks
+-------------------------------------------------------------------------------
+.. automodule:: sct_dbtool.sanity
+    :members:
+
+:mod:`sct_dbtool.setup` -- CLI setup entry-point
+-------------------------------------------------------------------------------
+.. automodule:: sct_dbtool.setup
+    :members:
+
+:mod:`sct_dbtool.main` -- Main CLI entry-point
+-------------------------------------------------------------------------------
+.. automodule:: sct_dbtool.main
+    :members:

sct_dbtool/sct_dbtool/__init__.py

@@ -0,0 +1,2 @@
+__author__ = 'Christian S. Perone'
+__version__ = '0.1'