Merge pull request #72 from c3g/develop

Release v0.4.0

.gitignore

@@ -22,3 +22,7 @@ env/
 # coverage
 .coverage
 htmlcov/
+
+# docs build
+
+docs/_build

.readthedocs.yml

@@ -0,0 +1,18 @@
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 0.4.0
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: docs/requirements.txt

chord_metadata_service/chord/api_views.py

@@ -1,6 +1,6 @@
 from rest_framework import viewsets
 from rest_framework.permissions import BasePermission, SAFE_METHODS
-from chord_metadata_service.phenopackets.api_views import LargeResultsSetPagination
+from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
 from .models import *
 from .permissions import OverrideOrSuperUserOnly
 from .serializers import *

chord_metadata_service/chord/views_ingest.py

@@ -99,7 +99,10 @@ def create_phenotypic_feature(pf):
     return pf_obj
 
 
+# Mounted on /private/, so will get protected anyway; this allows for access from WES
+# TODO: Ugly and misleading permissions
 @api_view(["POST"])
+@permission_classes([AllowAny])
 def ingest(request):
     # Private ingest endpoints are protected by URL namespace, not by Django permissions.
 

chord_metadata_service/chord/views_search.py

@@ -1,6 +1,5 @@
 import itertools
 from datetime import datetime
-import json
 
 from django.db import connection
 from django.conf import settings
@@ -167,6 +166,8 @@ def chord_search(request):
     return search(request, internal_data=False)
 
 
+# Mounted on /private/, so will get protected anyway; this allows for access from federation service
+# TODO: Ugly and misleading permissions
 @api_view(["POST"])
 @permission_classes([AllowAny])
 def chord_private_search(request):
@@ -262,13 +263,18 @@ def fhir_public_search(request):
     return fhir_search(request)
 
 
+# Mounted on /private/, so will get protected anyway
+# TODO: Ugly and misleading permissions
 @api_view(["POST"])
 @permission_classes([AllowAny])
 def fhir_private_search(request):
     return fhir_search(request, internal_data=True)
 
 
+# Mounted on /private/, so will get protected anyway; this allows for access from federation service
+# TODO: Ugly and misleading permissions
 @api_view(["POST"])
+@permission_classes([AllowAny])
 def chord_private_table_search(request, table_id):
     # Search phenopacket data types in specific tables
     # Private search endpoints are protected by URL namespace, not by Django permissions.

chord_metadata_service/metadata/settings.py

@@ -38,6 +38,8 @@
 
 # CHORD-specific settings
 
+CHORD_URL = os.environ.get("CHORD_URL", None)  # Leave None if not specified, for running in other contexts
+
 # SECURITY WARNING: Don't run with CHORD_PERMISSIONS turned off in production,
 # unless an alternative permissions system is in place.
 CHORD_PERMISSIONS = os.environ.get("CHORD_PERMISSIONS", str(not DEBUG)).lower() == "true"

chord_metadata_service/patients/api_views.py

@@ -1,4 +1,4 @@
-from rest_framework import viewsets, pagination
+from rest_framework import viewsets
 from rest_framework.settings import api_settings
 from .serializers import IndividualSerializer
 from .models import Individual
@@ -7,12 +7,7 @@
     FHIRRenderer,
     PhenopacketsRenderer
 )
-
-
-class LargeResultsSetPagination(pagination.PageNumberPagination):
-    page_size = 25
-    page_size_query_param = 'page_size'
-    max_page_size = 10000
+from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
 
 
 class IndividualViewSet(viewsets.ModelViewSet):

chord_metadata_service/phenopackets/api_views.py

@@ -1,14 +1,10 @@
-from rest_framework import viewsets, pagination
-from .serializers import *
-from .models import *
+from rest_framework import viewsets
 from rest_framework.settings import api_settings
-from chord_metadata_service.restapi.api_renderers import *
-
 
-class LargeResultsSetPagination(pagination.PageNumberPagination):
-    page_size = 25
-    page_size_query_param = 'page_size'
-    max_page_size = 10000
+from chord_metadata_service.restapi.api_renderers import *
+from chord_metadata_service.restapi.pagination import LargeResultsSetPagination
+from .serializers import *
+from .models import *
 
 
 class PhenopacketsModelViewSet(viewsets.ModelViewSet):

chord_metadata_service/restapi/pagination.py

@@ -0,0 +1,41 @@
+from django.conf import settings
+from rest_framework import pagination
+from urllib.parse import urljoin
+
+
+__all__ = [
+    "LargeResultsSetPagination",
+]
+
+
+class LargeResultsSetPagination(pagination.PageNumberPagination):
+    page_size = 25
+    page_size_query_param = 'page_size'
+    max_page_size = 10000
+
+    # Fix next/previous links inside sub-path-mounted reverse proxies in the CHORD context:
+
+    def _get_chord_absolute_uri(self):
+        full_path = self.request.get_full_path()
+        # Strip first slash if necessary, to avoid urljoin removing reverse proxy sub-paths
+        if len(full_path) > 0 and full_path[0] == "/":
+            full_path = full_path[1:]
+        return urljoin(settings.CHORD_URL, full_path)
+
+    def get_next_link(self):
+        if settings.CHORD_URL is not None:
+            # Monkey-patch rewrite build_absolute_uri
+            self.request.build_absolute_uri = self._get_chord_absolute_uri
+        return super(LargeResultsSetPagination, self).get_next_link()
+
+    def get_previous_link(self):
+        if settings.CHORD_URL is not None:
+            # Monkey-patch rewrite build_absolute_uri
+            self.request.build_absolute_uri = self._get_chord_absolute_uri
+        return super(LargeResultsSetPagination, self).get_previous_link()
+
+    def get_html_context(self):
+        if settings.CHORD_URL is not None:
+            # Monkey-patch rewrite build_absolute_uri
+            self.request.build_absolute_uri = self._get_chord_absolute_uri
+        super(LargeResultsSetPagination, self).get_html_context()

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+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)

docs/conf.py

@@ -0,0 +1,57 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- 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
+import django
+sys.path.insert(0, os.path.abspath('..'))
+os.environ['DJANGO_SETTINGS_MODULE'] = 'chord_metadata_service.metadata.settings'
+django.setup()
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'Metadata service'
+copyright = '2020, Ksenia Zaytseva, David Lougheed, Simon Chenard'
+author = 'Ksenia Zaytseva, David Lougheed, Simon Chenard'
+
+# The full version, including alpha/beta/rc tags
+release = '0.3.0'
+
+
+# -- General configuration ---------------------------------------------------
+
+# 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']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# 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 = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- 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'
+
+# 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']

docs/index.rst

@@ -0,0 +1,26 @@
+.. metadata service documentation master file, created by
+   sphinx-quickstart on Thu Feb 20 15:29:45 2020.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to metadata service's documentation!
+============================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   modules/introduction
+   modules/installation
+   modules/models
+   modules/views
+
+
+
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+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% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/modules/installation.rst

@@ -0,0 +1,52 @@
+Installation
+============
+
+1. Clone the project from github (use :code:`-r` to fetch submodules content)
+
+.. code-block::
+
+    git clone https://github.com/c3g/chord_metadata_service.git
+
+
+2. Install the git submodule for DATS JSON schemas (if you did not clone recursively):
+
+.. code-block::
+
+    git submodule update --init
+
+3. Create and activate virtual environment
+
+4. Cd to the main directory and install required packages:
+
+.. code-block::
+
+    pip install -r requirements.txt
+
+5. The service uses PostgreSQL database for data storage. Install PostgreSQL following `this tutorial <https://www.postgresql.org/docs/12/tutorial-install.html>`_.
+
+6. Configure database connection in settings.py
+
+e.g. settings if running database on localhost, default port for PostgreSQL is 5432:
+
+.. code-block:: python
+
+    DATABASES = {
+        'default': {
+            'ENGINE': 'django.db.backends.postgresql_psycopg2',
+            'NAME': 'database_name',
+            'USER': 'user',
+            'PASSWORD': 'password',
+            'HOST': 'localhost',
+            'PORT': '5432',
+        }
+    }
+
+7. From the main directory run (where the manage.py file located):
+
+.. code-block::
+
+    python manage.py makemigrations
+    python manage.py migrate
+    python manage.py runserver
+
+8. Development server runs at :code:`localhost:8000`