Merge pull request #520 from PoonLab/dev

Restore local database and fix bugs

.gitignore

@@ -22,3 +22,9 @@ cypress/plugins/
 *.yml
 !docker-compose.yml
 !docker_scripts/backend/*
+*.json
+*.xz
+working/*
+scripts/*
+covizu/data/xbb_outgrp.fasta
+

Dockerfile.backend

@@ -1,4 +1,4 @@
-FROM ubuntu:latest
+FROM ubuntu:22.04
 
 ENV DEBIAN_FRONTEND noninteractive
 
@@ -10,7 +10,7 @@ ENV OMPI_ALLOW_RUN_AS_ROOT=1 OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
 ADD https://bootstrap.pypa.io/get-pip.py /tmp/get-pip.py
 
 RUN python3.10 /tmp/get-pip.py
-RUN /usr/local/bin/pip install biopython mpi4py rpy2
+RUN /usr/local/bin/pip install biopython mpi4py rpy2 psycopg2-binary
 
 RUN R -e "install.packages('tidyquant',dependencies=TRUE, repos='http://cran.rstudio.com/')"
 RUN R -e "install.packages('matrixStats',dependencies=TRUE, repos='http://cran.rstudio.com/')"
@@ -32,7 +32,3 @@ RUN git clone --depth=1 https://github.com/neherlab/treetime.git /root/treetime
 RUN git clone --depth=1 https://github.com/somme89/rapidNJ.git /root/rapidnj && \
     make -C /root/rapidnj && \
     cp /root/rapidnj/bin/rapidnj /usr/local/bin
-
-RUN git clone https://github.com/PoonLab/covizu.git /root/covizu && \
-    git -C /root/covizu submodule init && \
-    git -C /root/covizu submodule update

Dockerfile.frontend

@@ -5,14 +5,13 @@ RUN mkdir -p /opt/app
 WORKDIR /opt/app
 COPY $basepath/package.json $basepath/package-lock.json .
 RUN npm install
-COPY $basepath/config/* config/
-COPY $basepath/js/* js/
-COPY $basepath/server/* server/
-COPY $basepath/data/* data/ 
-COPY $basepath/img/* img/ 
-COPY $basepath/css/* css/ 
-COPY $basepath/mongodb_scripts/* mongodb_scripts/
+COPY $basepath/config/ config/
+COPY $basepath/js/ js/
+COPY $basepath/server/ server/
+COPY $basepath/data/ data/ 
+COPY $basepath/img/ img/ 
+COPY $basepath/css/ css/ 
+COPY $basepath/mongodb_scripts/ mongodb_scripts/
 COPY $basepath/*.html $basepath/*.js .
 COPY .env* .
-EXPOSE $port
 CMD ["sh", "-c", "npm run delete-users && npm run create-users && npm run update-db1 && npm run start-db1"]

INSTALL.md

@@ -1,17 +1,18 @@
 ## Dependencies
 
-* [Python](https://www.python.org/) 3.6 or higher, and the following modules:
+* [Python](https://www.python.org/) 3.7 or higher, and the following modules:
   * [BioPython](https://biopython.org/) version 1.7+
   * [mpi4py](https://pypi.org/project/mpi4py/)
   * [SciPy](https://www.scipy.org/) version 1.5+
+  * [rpy2](https://rpy2.github.io/doc/latest/html/index.html) version 3.5.13+
+  * [psycopg2](https://pypi.org/project/psycopg2/) version 2.9.6+
 * [minimap2](https://github.com/lh3/minimap2) version 2.1+ 
 * [FastTree2](http://www.microbesonline.org/fasttree/) version 2.1.10+, compiled for [double precision](http://www.microbesonline.org/fasttree/#BranchLen)
 * [TreeTime](https://github.com/neherlab/treetime) version 0.7.5+
 * [RapidNJ](https://birc.au.dk/software/rapidnj/)
 * [git](https://git-scm.com/)
 * [Node.js](https://nodejs.org/en/download/) version 18.0.0+
 * [npm](https://docs.npmjs.com/about-npm-versions)
-* [rpy2](https://rpy2.github.io/doc/latest/html/index.html) version 3.5.13+
 * [R](https://cran.r-project.org/) (tested on 4.2.1) and the following packages:
   * [tidyquant](https://cran.r-project.org/web/packages/tidyquant/index.html)
   * [matrixStats](https://cran.rstudio.com/web/packages/matrixStats/index.html)
@@ -27,6 +28,8 @@ If running locally (without dedicated GISAID feed):
 
 ## Installation
 
+### Setup Back-End
+
 * Navigate to the directory in your filesystem under which you want to install the `covizu` directory
 
 * Clone the repository:
@@ -39,6 +42,36 @@ git clone https://github.com/PoonLab/covizu
 sudo python3 setup.py install  # omit `sudo` if you don't have superuser privileges
 ```
 
+* [Optional] Install PostgreSQL - [Database for Extracted Features](https://github.com/PoonLab/covizu/issues/485)
+  * [Download](https://www.postgresql.org/download/) and install PostgreSQL based on your operating system or pull the latest [docker image](https://hub.docker.com/_/postgres)
+  * The following environment variables must be defined:
+    * `POSTGRES_USER` - User name set up during installation of PostgreSQL
+    * `POSTGRES_PASSWORD` - Password for the given user name
+  * Optional environment variables:
+    * `POSTGRES_DB` - The desired database name to use for the analysis. The default database name is `gisaid_db`
+    * `POSTGRES_HOST` - The host name where PostgreSQL is running on. The default host is `localhost`
+    * `POSTGRES_PORT` - The port used by PostgreSQL. The default port number is `5432`
+
+* [Optional] Using Docker
+  * In the root directory, run the following command to build and start PostgreSQL. This will create a default network called `covizu_default`
+    ```
+    docker compose up -d postgres
+    ```
+  * In a `.env` file, include the following:
+    * `POSTGRES_HOST=postgres`
+    * `POSTGRES_USER=`
+    * `POSTGRES_PASSWORD=`
+  * Build the docker image from the `Dockerfile.backend` Dockerfile using the following command: 
+    ```
+    docker build --platform=linux/amd64 -t covizu-backend -f Dockerfile.backend .
+    ```
+  * Create a container named `backend` from the `covizu-backend` image using the following command: 
+    ```
+    docker run --name backend --volume ${PWD}:/root/covizu --network covizu_default --env-file .env -itd covizu-backend
+    ```
+
+### Setup Front-End
+
 If you're running the server (front-end) for the first time, obtain the following data files from our main server at 
 https://filogeneti.ca/covizu/data/:
 * `timetree.nwk`
@@ -90,12 +123,13 @@ Finally, run the following commands:
 
 Once you launch the local webserver with `npm start`, allow up to a minute for the server to initialize and then navigate your browser to `localhost:8001`.
 
+### Run Front-End Unit Tests
+
 To run the end-to-end tests with [Cypress](http://cypress.io) start the test server
 ```
 npm test
 ```
 and in a new terminal terminal window run 
 ```
-npx cypress run
-```
-
+npx cypress run --config-file "config/cypress.config.js"
+```