This is some content
+This is another sub-heading
""", + markdown_content) diff --git a/wqflask/tests/unit/wqflask/test_markdown_routes.py b/wqflask/tests/unit/wqflask/test_markdown_routes.py deleted file mode 100644 index 90e0f17c..00000000 --- a/wqflask/tests/unit/wqflask/test_markdown_routes.py +++ /dev/null @@ -1,54 +0,0 @@ -"""Test functions in markdown utils""" - -import unittest -from unittest import mock - -from dataclasses import dataclass -from wqflask.markdown_routes import render_markdown - - -@dataclass -class MockRequests404: - status_code: int = 404 - - -@dataclass -class MockRequests200: - status_code: int = 200 - content: str = b""" -# Glossary -This is some content - -## Sub-heading -This is another sub-heading""" - - -class TestMarkdownRoutesFunctions(unittest.TestCase): - """Test cases for functions in markdown_routes""" - - @mock.patch('wqflask.markdown_routes.requests.get') - def test_render_markdown_when_fetching_locally(self, requests_mock): - requests_mock.return_value = MockRequests404() - markdown_content = render_markdown("general/glossary/glossary.md") - requests_mock.assert_called_with( - "https://raw.githubusercontent.com" - "/genenetwork/gn-docs/" - "master/general/" - "glossary/glossary.md") - self.assertRegexpMatches(markdown_content, - "Content for general/glossary/glossary.md not available.") - - @mock.patch('wqflask.markdown_routes.requests.get') - def test_render_markdown_when_fetching_remotely(self, requests_mock): - requests_mock.return_value = MockRequests200() - markdown_content = render_markdown("general/glossary/glossary.md") - requests_mock.assert_called_with( - "https://raw.githubusercontent.com" - "/genenetwork/gn-docs/" - "master/general/" - "glossary/glossary.md") - self.assertEqual("""This is some content
-This is another sub-heading
""", - markdown_content) diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py index 8b2055cd..5758b13e 100644 --- a/wqflask/wqflask/__init__.py +++ b/wqflask/wqflask/__init__.py @@ -8,14 +8,14 @@ from flask import Flask from typing import Tuple from urllib.parse import urlparse from utility import formatting -from wqflask.markdown_routes import glossary_blueprint -from wqflask.markdown_routes import references_blueprint -from wqflask.markdown_routes import links_blueprint -from wqflask.markdown_routes import policies_blueprint -from wqflask.markdown_routes import environments_blueprint -from wqflask.markdown_routes import facilities_blueprint -from wqflask.markdown_routes import blogs_blueprint -from wqflask.markdown_routes import news_blueprint +from wqflask.api.markdown import glossary_blueprint +from wqflask.api.markdown import references_blueprint +from wqflask.api.markdown import links_blueprint +from wqflask.api.markdown import policies_blueprint +from wqflask.api.markdown import environments_blueprint +from wqflask.api.markdown import facilities_blueprint +from wqflask.api.markdown import blogs_blueprint +from wqflask.api.markdown import news_blueprint app = Flask(__name__) diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py index a135ecc8..9b875c99 100644 --- a/wqflask/wqflask/api/correlation.py +++ b/wqflask/wqflask/api/correlation.py @@ -9,7 +9,6 @@ from utility.db_tools import escape from wqflask.correlation import correlation_functions - def do_correlation(start_vars): assert('db' in start_vars) assert('target_db' in start_vars) @@ -26,7 +25,6 @@ def do_correlation(start_vars): corr_results = calculate_results( this_trait, this_dataset, target_dataset, corr_params) - #corr_results = collections.OrderedDict(sorted(corr_results.items(), key=lambda t: -abs(t[1][0]))) final_results = [] for _trait_counter, trait in enumerate(list(corr_results.keys())[:corr_params['return_count']]): @@ -54,11 +52,7 @@ def do_correlation(start_vars): "#_strains": num_overlap, "p_value": sample_p } - final_results.append(result_dict) - - # json_corr_results = generate_corr_json(final_corr_results, this_trait, this_dataset, target_dataset, for_api = True) - return final_results diff --git a/wqflask/wqflask/api/markdown.py b/wqflask/wqflask/api/markdown.py new file mode 100644 index 00000000..580b9ac0 --- /dev/null +++ b/wqflask/wqflask/api/markdown.py @@ -0,0 +1,186 @@ +"""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("/