Merge github.com:genenetwork/genenetwork2 into acenteno

5 files changed, 152 insertions, 0 deletions

diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md
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+---
+name: Bug report
+about: Create a report to help us improve
+title: '[Bug] Bug Title'
+labels: ''
+assignees: ''
+
+---
+
+**Describe the bug**
+<!-- A clear and concise description of what the bug is. -->
+
+**To Reproduce**
+<!-- Steps to reproduce the behavior -->
+
+**Expected behavior**
+<!-- A clear and concise description of what you expected to happen. -->
+
+**Screenshots**
+<!-- If applicable, add screenshots to help explain your problem. -->
+
+**Environment setup (please complete the following information):**
+<!-- - OS: [e.g. Linux] -->
+<!-- - Guix Version (optional) -->
+<!-- - [Anything else you think is relevant] -->
+
+**Additional context**
+<!-- Add any other context about the problem here. -->
diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md
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index 00000000..813974c1
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+++ b/.github/ISSUE_TEMPLATE/feature_request.md
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+---
+name: Feature request
+about: Suggest a new feature for this project(Very Specific)
+title: '[Feature] My-cool-feature'
+labels: ''
+assignees: ''
+
+---
+
+## Is your feature request related to a problem? Please describe.
+<!-- A clear and concise description of what the problem is. -->
+<!-- Example: I'm always frustrated when [...] -->
+
+## Describe the solution you'd like
+<!-- A clear and concise description of what you want to happen. -->
+
+## Describe alternatives you've considered
+<!-- A clear and concise description of any alternative solutions or features you've considered. -->
+
+## User Stories (optional)
+<!-- Example: -->
+<!-- As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ -->
+<!-- **Feature:** _[Brief description of feature]_ -->
+<!-- _[Any additional descriptions on feature]_ -->
+<!-- **Scenario:**
+Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_
+here -->
+
+## Additional context
+<!-- Add any other context or screenshots about the feature request here. -->
diff --git a/.github/ISSUE_TEMPLATE/user_story.md b/.github/ISSUE_TEMPLATE/user_story.md
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index 00000000..d46976ba
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+---
+name: User Story
+about: Suggest an idea for this project
+title: ['Feature] My-cool-new-feature'
+labels: ''
+assignees: ''
+
+---
+<!-- As a _[role or persona]_, I want _[goal/ need]_ so that _[why]_ -->
+<!-- **Feature:** _[Brief description of feature]_ -->
+<!-- _[Any additional descriptions on feature]_ -->
+<!-- **Scenario:** Please use _[Gherkin](https://cucumber.io/docs/gherkin/reference/)_ here -->
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
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+++ b/.github/PULL_REQUEST_TEMPLATE.md
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+#### Description
+<!--Brief description of the PR. What does this PR do? -->
+
+#### How should this be tested?
+<!-- What should you do to test this PR? Is there any manual quality
+assurance checks that should be done. What are the expectations -->
+
+#### Any background context you want to provide?
+<!-- Anything the reviewer should be aware of ahead of testing -->
+
+#### What are the relevant pivotal tracker stories?
+<!-- Does this PR track anything anywhere? -->
+
+#### Screenshots (if appropriate)
+
+#### Questions
+<!-- Are there any questions for the reviewer -->
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
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index 00000000..8e2c7966
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+++ b/.github/workflows/main.yml
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+name: tests
+
+# Run actions when pushing to the testing branch or when you create a
+# PR against it
+on:
+  push:
+    branches: [ testing ]
+  pull_request:
+    branches: [ testing ]
+
+jobs:
+  unittest:
+    runs-on: ubuntu-latest
+    container: bonfacekilz/genenetwork2:latest
+
+    steps:
+    # First start with mariadb set then checkout. The checkout gives
+    # the mysqld enough time to start
+    - name: Set up mariadb
+      run: |
+        mysql_install_db --user=mysql --datadir=/usr/local/mysql
+        # Wait for the mysqld_safe process to start
+        mysqld_safe --user=mysql --datadir=/usr/local/mysql &
+
+    # Use v1 of checkout since v2 fails
+    - name: Checkout Project
+      uses: actions/checkout@v1
+
+    # Redis is required by some of the tests 6379
+    - name: Start Redis
+      run: |
+        /gn2-profile/bin/screen -dmLS redisconn /gn2-profile/bin/redis-server
+
+    # Initialise the tables
+    - name: Bootstrap tables
+      run: |
+        mysql -u root -e "SHOW DATABASES;"
+        mysql -u root -e "CREATE DATABASE db_webqtl_s;"
+        mysql -u root -e "CREATE USER 'gn2'@'localhost' IDENTIFIED BY 'mysql_password';"
+        mysql -u root -e "GRANT ALL PRIVILEGES ON *.* TO 'gn2'@'localhost';FLUSH PRIVILEGES;"
+
+    - name: Start Genenetwork as a  Background Task
+      run: |
+        /gn2-profile/bin/screen -dm bash -c "env GN2_PROFILE=/gn2-profile \
+        TMPDIR=/tmp SERVER_PORT=5004 \
+        WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
+        GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
+        etc/default_settings.py"
+
+    - name: Run the unit tests
+      run: |
+        env GN2_PROFILE=/gn2-profile \
+        TMPDIR=/tmp SERVER_PORT=5004 \
+        WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
+        GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
+        etc/default_settings.py -c -m unittest discover -v
+
+    # - name: Test for Broken Links
+    #   run: |
+    #     env GN2_PROFILE=/gn2-profile \
+    #     TMPDIR=/tmp\
+    #     WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG \
+    #     GENENETWORK_FILES=/genotype_files/ bin/genenetwork2 \
+    #     etc/default_settings.py -c \
+    #     $PWD/test/requests/links_scraper/genelinks.py