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"""Markdown routes
Render pages from github, or if they are unavailable, look for it else where
"""
import requests
import markdown
import os
import sys
from bs4 import BeautifulSoup # type: ignore
from flask import send_from_directory
from flask import Blueprint
from flask import render_template
from typing import Dict
from typing import List
glossary_blueprint = Blueprint('glossary_blueprint', __name__)
references_blueprint = Blueprint("references_blueprint", __name__)
environments_blueprint = Blueprint("environments_blueprint", __name__)
links_blueprint = Blueprint("links_blueprint", __name__)
policies_blueprint = Blueprint("policies_blueprint", __name__)
facilities_blueprint = Blueprint("facilities_blueprint", __name__)
news_blueprint = Blueprint("news_blueprint", __name__)
blogs_blueprint = Blueprint("blogs_blueprint", __name__)
def render_markdown(file_name, is_remote_file=True):
"""Try to fetch the file name from Github and if that fails, try to
look for it inside the file system """
github_url = ("https://raw.githubusercontent.com/"
"genenetwork/gn-docs/master/")
if not is_remote_file:
text = ""
with open(file_name, "r", encoding="utf-8") as input_file:
text = input_file.read()
return markdown.markdown(text,
extensions=['tables'])
md_content = requests.get(f"{github_url}{file_name}")
if md_content.status_code == 200:
return markdown.markdown(md_content.content.decode("utf-8"),
extensions=['tables'])
return (f"\nContent for {file_name} not available. "
"Please check "
"(here to see where content exists)"
"[https://github.com/genenetwork/gn-docs]. "
"Please reach out to the gn2 team to have a look at this")
def get_file_from_python_search_path(pathname_suffix):
cands = [os.path.join(d, pathname_suffix) for d in sys.path]
try:
return list(filter(os.path.exists, cands))[0]
except IndexError:
return None
def get_blogs(user: str = "genenetwork",
repo_name: str = "gn-docs") -> dict:
blogs: Dict[int, List] = {}
github_url = f"https://api.github.com/repos/{user}/{repo_name}/git/trees/master?recursive=1"
repo_tree = requests.get(github_url).json()["tree"]
for data in repo_tree:
path_name = data["path"]
if path_name.startswith("blog") and path_name.endswith(".md"):
split_path = path_name.split("/")[1:]
try:
year, title, file_name = split_path
except Exception as e:
year, file_name = split_path
title = ""
subtitle = os.path.splitext(file_name)[0]
blog = {
"title": title,
"subtitle": subtitle,
"full_path": path_name
}
if year in blogs:
blogs[int(year)].append(blog)
else:
blogs[int(year)] = [blog]
return dict(sorted(blogs.items(), key=lambda x: x[0], reverse=True))
@glossary_blueprint.route('/')
def glossary():
return render_template(
"glossary.html",
rendered_markdown=render_markdown("general/glossary/glossary.md")), 200
@references_blueprint.route('/')
def references():
return render_template(
"references.html",
rendered_markdown=render_markdown("general/references/references.md")), 200
@news_blueprint.route('/')
def news():
return render_template(
"news.html",
rendered_markdown=render_markdown("general/news/news.md")), 200
@environments_blueprint.route("/")
def environments():
md_file = get_file_from_python_search_path("wqflask/DEPENDENCIES.md")
svg_file = get_file_from_python_search_path(
"wqflask/dependency-graph.html")
svg_data = None
if svg_file:
with open(svg_file, 'r') as f:
svg_data = "".join(
BeautifulSoup(f.read(),
'lxml').body.script.contents)
if md_file is not None:
return (
render_template("environment.html",
svg_data=svg_data,
rendered_markdown=render_markdown(
md_file,
is_remote_file=False)),
200
)
# Fallback: Fetch file from server
return (render_template(
"environment.html",
svg_data=None,
rendered_markdown=render_markdown(
"general/environments/environments.md")),
200)
@environments_blueprint.route('/svg-dependency-graph')
def svg_graph():
directory, file_name, _ = get_file_from_python_search_path(
"wqflask/dependency-graph.svg").partition("dependency-graph.svg")
return send_from_directory(directory, file_name)
@links_blueprint.route("/")
def links():
return render_template(
"links.html",
rendered_markdown=render_markdown("general/links/links.md")), 200
@policies_blueprint.route("/")
def policies():
return render_template(
"policies.html",
rendered_markdown=render_markdown("general/policies/policies.md")), 200
@facilities_blueprint.route("/")
def facilities():
return render_template("facilities.html", rendered_markdown=render_markdown("general/help/facilities.md")), 200
@blogs_blueprint.route("/<path:blog_path>")
def display_blog(blog_path):
return render_template("blogs.html", rendered_markdown=render_markdown(blog_path))
@blogs_blueprint.route("/")
def blogs_list():
blogs = get_blogs()
return render_template("blogs_list.html", blogs=blogs)
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