Merge branch 'release/0.2.0'

.envs/.local/.django

@@ -21,10 +21,11 @@ LZ_OFFICIAL_DOMAIN=localhost:8000
 # ------------------------------------------------------------------------------
 GOOGLE_ANALYTICS_ID=
 
-# Sentry uses two buckets: one for python errors (backend) and one for JS (frontend)
+# Our Sentry configuration uses two buckets: one for python errors (backend) and one for JS (frontend)
 # ------------------------------------------------------------------------------
 SENTRY_DSN=
 SENTRY_DSN_FRONTEND=
 
 # Set the location of download large lookup files (which are downloaded separately, after the build step)
+# This path is relative to the docker container
 ZORP_ASSETS_DIR=/app/.lookups

.envs/.production/.django-sample

@@ -0,0 +1,60 @@
+##### Example file. Rename to .django to use in production
+
+# General
+# ------------------------------------------------------------------------------
+# DJANGO_READ_DOT_ENV_FILE=True
+DJANGO_SETTINGS_MODULE=config.settings.production
+DJANGO_SECRET_KEY=
+# The admin site has restricted functionality, but make it hard for bots to find. In the future this could be served separately behind a VPN
+DJANGO_ADMIN_URL=admin-changeme-something-very-hard-to-guess/
+# The localhost entries work if we are using a reverse proxy
+DJANGO_ALLOWED_HOSTS=.my.locuszoom.org,localhost,localhost:5000
+LZ_OFFICIAL_DOMAIN=my.locuszoom.org
+
+# Security
+# ------------------------------------------------------------------------------
+# TIP: It is better to handle the redirect via the server. However, django can handle the redirect if needed.
+DJANGO_SECURE_SSL_REDIRECT=False
+
+# Email
+# ------------------------------------------------------------------------------
+[email protected]
+
+DJANGO_EMAIL_HOST=smtp.host.example
+DJANGO_EMAIL_HOST_USER=locuszoom-noreply
+DJANGO_EMAIL_HOST_PASSWORD=
+
+# django-allauth
+# ------------------------------------------------------------------------------
+# This can be disabling if, eg, you are running a private instance and don't want random people to upload things
+DJANGO_ACCOUNT_ALLOW_REGISTRATION=True
+
+# Gunicorn
+# ------------------------------------------------------------------------------
+# Recommend 2-4x # cores
+WEB_CONCURRENCY=8
+
+# Our Sentry configuration uses two buckets: one for python errors (backend) and one for JS (frontend)
+# ------------------------------------------------------------------------------
+SENTRY_DSN=
+SENTRY_DSN_FRONTEND=
+
+# Google Analytics
+# ------------------------------------------------------------------------------
+GOOGLE_ANALYTICS_ID=
+
+# Redis
+# ------------------------------------------------------------------------------
+REDIS_URL=redis://redis:6379/0
+
+# Celery
+# ------------------------------------------------------------------------------
+
+# Flower
+## Set these to very hard to guess values
+CELERY_FLOWER_USER=
+CELERY_FLOWER_PASSWORD=
+CELERY_WORKERS=12
+
+# For now, re-use the local "uploads" mount point as a place to store the large lookup files required by annotations
+ZORP_ASSETS_DIR=/lz-uploads/.lookups

.envs/.production/.postgres-sample

@@ -0,0 +1,8 @@
+# PostgreSQL
+# ------------------------------------------------------------------------------
+POSTGRES_HOST=postgres
+POSTGRES_PORT=5432
+POSTGRES_DB=locuszoom_plotting_service
+# Please make sure to set these.
+POSTGRES_USER=
+POSTGRES_PASSWORD=

.gitignore

@@ -9,8 +9,7 @@ celerybeat.pid
 staticfiles/
 
 # Webpack built assets (and files that reference them)
-assets/webpack_bundles/
-webpack-stats.json
+locuszoom_plotting_service/static/webpack_bundles/
 
 # Sphinx documentation
 docs/_build/
@@ -43,3 +42,7 @@ scripts/data_loaders/sources/*
 # Configuration files that should not be checked into Git
 .envs/*
 !.envs/.local/
+# Exclude production envs, EXCEPT samples
+!.envs/.production/
+.envs/.production/*
+!.envs/.production/*sample

.nvmrc

@@ -1 +1 @@
-lts/erbium
+lts/fermium

README.md

@@ -1,6 +1,6 @@
 # LocusZoom: Hosted Upload Service
 
-Upload and share GWAS results with LocusZoom.js
+Upload, analyze, and share GWAS results with LocusZoom.js. Try it at [my.locuszoom.org](https://my.locuszoom.org).
 
 
 ## Settings
@@ -11,10 +11,11 @@ For a basic guide to most settings, see the [cookiecutter-django docs](https://c
 
 
 ### Quickstart
-The following commands will start a development environment. Some IDEs (such as Pycharm) are able to run the app via
- run configurations, which may be more convenient than starting things through the terminal. 
+The following commands will start a development environment. Some IDEs (such as Pycharm) are able to run the app via run configurations, which may be more convenient than starting things through the terminal.
+
+For production deployment instructions, see [docs/deploy/index.md](docs/deploy/index.md). 
 
-- In one tab, build assets: 
+- In one tab, build assets (in local development, this is currently done on the host system, outside of Docker): 
 
 `$ yarn run prod`
 
@@ -25,12 +26,15 @@ or with live rebuilding, if you intend to be changing JS code as you work:
 - In a second open terminal::
 
 ```
-$ docker-compose -f local.yml build
+$ docker system prune && docker-compose -f local.yml build --pull
 $ docker-compose -f local.yml up
 ```
 
-On the first installation, you will also need to download some large asset files required for annotations. (see 
-deployment docs for the correct command to use with production assets)
+(`docker system prune` is optional, but it can save your hard drive from filling up as you experiment with different build options)
+
+On the first installation, you will also need to download some large asset files required for annotations. For local development, a "test" version is available that will only annotate a limited subset of biologically interesting genes; this subset is much smaller than the full database, and easier to use on a laptop.
+
+(see deployment docs for the correct command to use with production assets)
 
 ```bash
 $ docker-compose -f local.yml run --rm django zorp-assets download --type snp_to_rsid_test --tag genome_build GRCh37 --no-update
@@ -63,8 +67,7 @@ into your browser. Now the user's email should be verified and ready to go.
 
 `$ docker-compose -f local.yml run --rm django python manage.py makemigrations`
 
-Then verify the migration file is correct, and restart docker to apply the migrations automatically.
-(in production, you must apply the migrations manually; see deployment guide for details)
+Then verify the migration file is correct, and restart Docker to apply the migrations automatically. (in production, you must apply the migrations manually; see deployment guide for details)
 
 
 ## Development and testing helpers
@@ -78,7 +81,7 @@ This script generates fake studies for search results, but it notably does not r
  It may be improved in the future to generate more realistic and complete fake data. 
 
 ### Opening a terminal for debugging
-Because all development happens inside a docker container, it is sometimes useful to open a terminal for debugging
+Because all development happens inside a Docker container, it is sometimes useful to open a terminal for debugging
 purposes. This can be done as follows.
 
 On a running container::
@@ -114,55 +117,18 @@ A suite of unit tests is available::
 
 `$ docker-compose -f local.yml run --rm django pytest`
 
-## Celery
-
-This app comes with Celery. The docker configuration will automatically launch celery workers when the app starts, but 
-the commands below may be useful when running the app in other environments.
-
-To run a celery worker:
-
-```bash
-$ cd locuszoom_plotting_service
-$ celery -A locuszoom_plotting_service.taskapp worker -l info
-```
-
-Please note: For Celery's import magic to work, it is important *where* the celery commands are run. If you are in the
-same folder with *manage.py*, you should be ok.
-
-
 ## Sentry
 
 Sentry is an error logging aggregator service. If a key (DSN) is provided in your .env file, errors will be tracked
- automatically. You will need one DSN each for your frontend (JS) and backend (python) code.
+ automatically.
 
 ## Deployment
 
 ### Docker
-This app uses docker to manage dependencies and create a working environment. See 
+This app uses Docker to manage dependencies and create a working environment. See 
 [deployment documentation](docs/deploy/index.md) for instructions on how to create a working, production server 
-environment. A local, debug-friendly docker configuration is also provided in this repo, and many of the instructions 
+environment. A local, debug-friendly Docker configuration is also provided in this repo, and many of the instructions 
 in this document assume this is what you will use. 
 
- The original docker configuration has been modified from cookiecutter-django; see their docs for more information 
+ The original Docker configuration has been modified from cookiecutter-django; see their docs for more information 
  about default options and design choices.  
-
-
-### (future) Initializing the app with default data
-
-Certain app features, such as "tagging datasets", will require loading initial data into the database.
-
-This feature is not yet used in production, but the notes below demonstrate loader scripts in progress.
-
-These datasets may be large or restricted by licensing rules; as such, they are not distributed with the code and must
-be downloaded/reprocessed separately for loading.
-
-- [SNOMED CT (Core) / May 2019](https://www.nlm.nih.gov/research/umls/Snomed/core_subset.html)
-
-These files must be downloaded separately due to license issues (they cannot be distributed with this repo).
-Run the appropriate scripts in `scripts/data_loaders/` to transform them into a format suitable for django usage.
-
-After creating the app, run the following command (once) to load them in (using the appropriate docker-compose file)::
-
-`$ docker-compose -f local.yml run --rm django python3 manage.py loaddata scripts/data_loaders/sources/snomed.json`
-
-[![Built with Cookiecutter Django](https://img.shields.io/badge/built%20with-Cookiecutter%20Django-ff69b4.svg)](https://github.com/pydanny/cookiecutter-django/)

assets/js/pages/gwas_summary.js

@@ -6,7 +6,7 @@ import {create_qq_plot, create_gwas_plot} from '../util/pheweb_plots';
 
 import Tabulator from 'tabulator-tables';
 import 'tabulator-tables/dist/css/bootstrap/tabulator_bootstrap4.css';
-import { pairs, sortBy } from 'underscore';
+import { toPairs, sortBy } from 'lodash';
 
 function createTopHitsTable(selector, data, region_url) {
     // Filter the manhattan json to a subset of just peaks, largest -log10p first
@@ -95,7 +95,7 @@ if (window.template_args.ingest_status === 2) {
                 return resp.json();
             })
             .then(data => {
-                sortBy(pairs(data.overall.gc_lambda), function (d) {
+                sortBy(toPairs(data.overall.gc_lambda), function (d) {
                     return -d[0];
                 }).forEach(function (d, i) {
                     // FIXME: Manually constructed HTML; change
@@ -111,7 +111,8 @@ if (window.template_args.ingest_status === 2) {
                 } else {
                     create_qq_plot([{ maf_range: [0, 0.5], qq: data.overall.qq, count: data.overall.count }], data.ci);
                 }
-            }).catch(() => {
+            }).catch((e) => {
+                console.error(e);
                 document.getElementById('qq_plot_container').textContent = 'Could not fetch QQ plot data.';
             });
     });