Merge pull request #32 from phac-nml/development

Release 2.1.0

.github/workflows/ci-tests.yml

@@ -0,0 +1,105 @@
+name: Integration Tests
+
+on:
+  pull_request: # Run on all pull requests
+  push:
+    branches:   # Run on any push to development or main
+      - development
+      - main
+  schedule:     # Run weekly on development and main
+    - cron: 0 2 * * 1
+      branches: development
+    - cron: 0 2 * * 1
+      branches: main
+
+
+jobs:
+  build-unittests:
+    runs-on: ubuntu-20.04 #See pre-installed software at https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md
+    strategy:
+      fail-fast: False #Setting so that if one of the test suites fail, the other will continue
+      matrix:
+        python-version: [ 3.6 ]
+
+    steps:
+      - uses: actions/checkout@v2 #Checkout the project from git
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Run Unit Tests
+        run: make unittests
+
+  build-irida-integration:
+    runs-on: ubuntu-20.04 #See pre-installed software at https://github.com/actions/virtual-environments/blob/main/images/linux/Ubuntu2004-README.md
+    env:
+      MYSQL_PORT: 3306
+      MYSQL_USER: test
+      MYSQL_PASSWORD: test
+      MYSQL_DATABASE: irida_importer_test
+      MYSQL_HOST: 127.0.0.1
+      MYSQL_ROOT_PASSWORD: password
+      NODE_OPTIONS: "--max-old-space-size=4096"
+      CONDA_PREFIX: /usr/share/miniconda
+
+    strategy:
+      fail-fast: False #Setting so that if one of the test suites fail, the other will continue
+      matrix:
+        branch: ['main','development'] # IRIDA Branches to test against
+
+    steps:
+      - uses: actions/checkout@v2 #Checkout the project from git
+      - name: Setup MySQL
+        uses: mirromutth/mysql-action@v1.1
+        with:
+          host port: ${{ env.MYSQL_PORT }}
+          character set server: 'utf8'
+          collation server: 'utf8_general_ci'
+          mysql version: '5.7'
+          mysql database: ${{ env.MYSQL_DATABASE }}
+          mysql user: ${{ env.MYSQL_USER }}
+          mysql password: ${{ env.MYSQL_PASSWORD }}
+          mysql root password: ${{ env.MYSQL_ROOT_PASSWORD }} #The root superuser password
+      - name: Verify MySQL connection
+        timeout-minutes: 10
+        run: |
+          while ! mysqladmin ping -h"${{ env.MYSQL_HOST }}" -P"${{ env.MYSQL_PORT }}" --silent; do
+            sleep 1
+          done
+      - name: Set up JDK 11 # Installs java 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: 11
+      - name: MySQL Setup (SUDO) # Sets ONLY_FULL_GROUP_BY flag and gives runner privileges over database
+        run: |
+          sudo mysql -e "SET GLOBAL sql_mode=(SELECT REPLACE(@@sql_mode,'ONLY_FULL_GROUP_BY',''));" -h ${{ env.MYSQL_HOST }} -P ${{ env.MYSQL_PORT }} -p${{ env.MYSQL_ROOT_PASSWORD }};
+          sudo mysql -e "CREATE USER '${{ env.MYSQL_USER }}'@'%' IDENTIFIED BY '${{ env.MYSQL_PASSWORD }}'; GRANT ALL ON ${{ env.MYSQL_DATABASE }}.* to '${{ env.MYSQL_USER }}'@'%';" -h ${{ env.MYSQL_HOST }} -P ${{ env.MYSQL_PORT }} -p${{ env.MYSQL_ROOT_PASSWORD }};
+      - name: Set up PostgreSQL
+        run: |
+          sudo apt-get update
+          sudo apt-get install postgresql libpq-dev
+          sudo service postgresql start
+          sudo -u postgres createuser --superuser "$USER"
+          createdb runner
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          auto-update-conda: true
+          python-version: 3.6.7
+          activate-environment: __irida_importer_py3.6.7
+      - name: Conda info
+        shell: bash -l {0}
+        run: conda info
+      - name: Install conda packages
+        shell: bash -l {0}
+        run: |
+          conda config --add channels defaults
+          conda config --add channels conda-forge
+          conda config --add channels bioconda
+          conda config --add channels iuc
+          conda install bioblend=0.13.0 oauthlib=3.0.1 requests=2.22.0 requests-oauthlib=1.2.0 simplejson=3.8.1
+      - name: Setup galaxy conda env
+        shell: bash -l {0}
+        run: conda create --name _galaxy_ python=3.7.6
+      - name: Run Integration Tests ${{ matrix.branch }}
+        timeout-minutes: 60
+        run: make integrationtests branch=${{ matrix.branch }} db_host=${{ env.MYSQL_HOST }} db_port=${{ env.MYSQL_PORT }}

.gitignore

@@ -15,3 +15,6 @@ env
 /.venv
 miniconda*
 .vscode
+.virtualenv
+irida_import.egg-info
+irida_import/tests/integration/tmp

CHANGELOG.md

@@ -2,6 +2,11 @@
 
 All notable changes to irida-galaxy-importer will be documeted in this file.
 
+## 2.1.0
+* Added in support for importing IRIDA files that are not available locally (i.e. in the cloud)
+* Switched from travisCI tests to Github Actions
+* Switched integration tests to launch irida via gradle
+
 ## 2.0.0
 
 * Added support for Python 3, while maintaining Python 2 support

Makefile

@@ -0,0 +1,34 @@
+SHELL=/bin/bash
+IRIDA_VERSION?=main
+
+requirements: clean env
+	source .virtualenv/bin/activate
+	python3 -m pip install -e .
+
+clean:
+	rm -rf irida_import/.pytest_cache
+	rm -rf .virtualenv
+	rm -rf irida_import.egg-info/
+	find -name "*pyc" -delete
+	rm -rf /tmp/repos
+	rm -rf irida_import/tests/integration/tmp
+	rm -rf venv
+
+env:
+	python3 -m venv .virtualenv
+	source .virtualenv/bin/activate
+	python3 --version
+	python3 -m pip install --upgrade wheel pip
+
+unittests: clean env
+	source .virtualenv/bin/activate
+	pip3 install -e .
+	pip3 install pytest
+	pytest irida_import/tests/unit/*.py
+
+integrationtests: clean env
+	source .virtualenv/bin/activate
+	python3 -m pip install -e .[TEST]
+	python3 -m pip install pytest
+	mkdir /tmp/repos
+	python3 irida_import/tests/integration/start_integration_tests.py $(branch) $(db_host) $(db_port)

README.md

@@ -68,7 +68,7 @@ The Galaxy [tools/][galaxy-tools] directory contains tools that come with the Ga
 ```bash
 cd galaxy/tools/
 
-git clone -b master https://github.com/phac-nml/irida-galaxy-importer.git
+git clone -b main https://github.com/phac-nml/irida-galaxy-importer.git
 cd irida-galaxy-importer
 
 # Optional. Checkout specific release from https://github.com/phac-nml/irida-galaxy-importer/releases
@@ -181,7 +181,7 @@ You will next want to make the appropriate changes with your connection informat
 
 ### MODIFY THESE ###
 admin_key: d9c54f0b38b75dd6513035e4dd786a0b
-galaxy_url: http://localhost:48888
+galaxy_url: http://127.0.0.1:48888
 ####################
 
 illumina_path: /illumina_reads
@@ -196,7 +196,7 @@ client_http_retry_delay: 30
 ### MODIFY THESE ###
 client_secret: qlB82t7Ct917127lL7oQ82bd9o2iAP8bT0rJohpz7s
 client_id: galaxy
-irida_url: http://localhost:8080
+irida_url: http://127.0.0.1:8080
 ####################
 
 initial_endpoint_suffix: /projects
@@ -246,7 +246,7 @@ If you wish to make additions to the code, the below instructions can be used to
 The script `run-tests.sh` can be used to run the tests. This should check for some of the dependencies and let you know which is missing. However, you will have to have the following dependencies installed:
 
 * Java 11
-* Maven
+* Gradle
 * MySQL/MariaDB (Server and Client)
 * PostgreSQL (Server and Client)
 * Git
@@ -256,7 +256,7 @@ The script `run-tests.sh` can be used to run the tests. This should check for so
 On Ubuntu, you can install these with:
 
 ```bash
-sudo apt-get install openjdk-11-jdk maven mariadb-client mariadb-server postgresql git chromium-chromedriver xvfb
+sudo apt-get install openjdk-11-jdk gradle mariadb-client mariadb-server postgresql git chromium-chromedriver xvfb
 ```
 
 MySQL must be configured to grant all privileges to the user `test` with password `test` for the databases `irida_test`. MySQL must also be configured to disable `ONLY_FULL_GROUP_BY` mode.
@@ -268,25 +268,18 @@ mysql -u root -e "SET GLOBAL sql_mode=(SELECT REPLACE(@@sql_mode,'ONLY_FULL_GROU
 ```
 
 ## 3.2. Running tests
-
-To run all the test, you can run:
-
-```bash
-./run-tests.sh
-```
-
-If you just want to run just the unit tests (much quicker) you can do:
+Unit tests can be run with:
 
 ```bash
-./run-tests.sh unit
+make unittests
 ```
 
-If you just want to run just the integration tests you can do:
+Integration tests can be run with
 
 ```bash
-./run-tests.sh integration
+make integrationtests branch=main
 ```
-
+This tests against the `main` branch of IRIDA
 
 [galaxy]: https://galaxyproject.org/
 [irida]: https://www.irida.ca/

irida_import/extras/apache2/index.html

@@ -27,7 +27,7 @@
 	}).config(function($sceDelegateProvider) {
 		$sceDelegateProvider.resourceUrlWhitelist([
     			'self',
-    			'http://localhost/**'
+    			'http://127.0.0.1/**'
   		]);
 	}).controller('galaxyController', ['$scope', '$http', '$window', '$location','$timeout', galaxyController]);
 
@@ -73,9 +73,9 @@
 
 		sampleFilePaths = [
 			"http://www.dgfdg.com/sample1file1",		
-			"file://localhost/home/jthiessen/lib_imp_dir/test/test.fastq"
+			"file://127.0.0.1/home/jthiessen/lib_imp_dir/test/test.fastq"
 			];
-		addSample("thisissample1'sname","http://localhost/some_IRIDA_API_path/Projects/1/Samples/1",sampleFilePaths);		
+		addSample("thisissample1'sname","http://127.0.0.1/some_IRIDA_API_path/Projects/1/Samples/1",sampleFilePaths);
 		$timeout(
 			function(){
 				document.getElementById("samplesSubmit").submit();

irida_import/extras/nginx/nginx.conf

@@ -2,7 +2,7 @@ events {}
 
 http {
     upstream galaxy_app {
-        server localhost:8888;
+        server 127.0.0.1:8888;
     }
 
     server {