Containerized the Interface and Visualization And Setup Github Actions

.github/linters/.pylintrc

@@ -92,6 +92,8 @@ disable=print-statement,
         setslice-method,
         import-error,
         no-absolute-import,
+        wrong-import-order,
+        wildcard-import,
         no-name-in-module,
         old-division,
         dict-iter-method,
@@ -135,7 +137,20 @@ disable=print-statement,
         xreadlines-attribute,
         deprecated-sys-function,
         exception-escape,
-        comprehension-escape
+        comprehension-escape,
+        invalid-name,
+        broad-except,
+        superfluous-parens,
+        missing-module-docstring,
+        missing-class-docstring
+        missing-function-docstring,
+        inconsistent-return-statements,
+        redefined-outer-name,
+        line-too-long,
+        bad-continuation,
+        trailing-newlines,
+        trailing-whitespace,
+        bad-whitespace
 
 # Enable the message, report, category or checker with the given id(s). You can
 # either give multiple identifier separated by comma (,) or put this option

.github/workflows/interface_test.yml

@@ -0,0 +1,37 @@
+name: YABA app tests
+
+on:
+  push:
+    branches: [ master, containerize ]
+  pull_request:
+    branches: [ master, containerize ]
+
+jobs:
+  interface_test:
+
+    runs-on: ubuntu-latest
+    defaults:
+        run:
+          working-directory: interface
+
+    strategy:
+      matrix:
+        node-version: [12.x, 14.x]
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v2
+
+    - name: Set up Node.js ${{ matrix.node-version }}
+      uses: actions/setup-node@v1
+      with:
+        node-version: ${{ matrix.node-version }}
+
+    - name: Install dependencies
+      run: npm install
+
+    - name: Run the tests and generate coverage report
+      run: npm test -- --coverage
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v1

.github/workflows/py_tests.yml

@@ -0,0 +1,55 @@
+# This workflow will install Python dependencies, run tests and lint with a single version of Python
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: YABA app tests
+
+on:
+  push:
+    branches: [ master, containerize ]
+  pull_request:
+    branches: [ master, containerize ]
+
+jobs:
+  app_test:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        code: [ app, client]
+        include:
+         - code: app
+           path: ./yaba_test/test_yaba.py
+         - code: client
+           path: ./yaba_client_test/test_yaba_client.py
+
+    steps:
+      - name: Checkout Code
+        uses: actions/checkout@v2
+
+      - name: Set up Python 3.7
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.7
+
+      - name: Install dependencies
+        run: |
+              pip install --upgrade pip
+              pip install pytest
+              pip install pytest-cov
+              pip install docker-compose
+
+      - name: Set-up the project
+        run: |
+              docker-compose up -d postgres
+              docker-compose run --rm bety initialize
+              docker-compose run --rm bety sync
+              docker-compose up -d
+              docker ps -a
+
+      - name: Test with pytest and generate coverage report
+        run: |
+              sleep 20
+              pytest --cov= ${{ matrix.path }} --cov-report=xml
+
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v1

client/client.py

@@ -3,14 +3,13 @@
 #################
 
 import requests
-from flask import Flask, g, render_template,request,redirect,Response,flash,jsonify, make_response
+from flask import Flask, render_template,request,redirect,Response,flash
 from flask import request
 
 import logging
-import json
 from time import sleep
-import sys
-from flask_cors import CORS, cross_origin
+
+from flask_cors import CORS
 
 # Create app
 app = Flask(__name__)

yaba_client_test/test_yaba_client.py

@@ -11,7 +11,7 @@ class BasicTests(unittest.TestCase):
 
     def test_insert_experiments(self):
         csv_filename = 'experiments.csv'
-        csv_path = '../input_files/experiments.csv'
+        csv_path = 'input_files/experiments.csv'
         files = {'fileName': open(csv_path, 'rb')}
         response = requests.post(
             'http://0.0.0.0:6001/experiments?username=guestuser', files=files)
@@ -20,12 +20,12 @@ def test_insert_experiments(self):
 
     def test_insert_sites(self):
         csv_filename = 'sites.csv'
-        csv_path = '../input_files/'+csv_filename
+        csv_path = 'input_files/'+csv_filename
 
-        shp_file = '../input_files/S8_two_row_polys.shp'
-        dbf_file = '../input_files/S8_two_row_polys.dbf'
-        prj_file = '../input_files/S8_two_row_polys.prj'
-        shx_file = '../input_files/S8_two_row_polys.shx'
+        shp_file = 'input_files/S8_two_row_polys.shp'
+        dbf_file = 'input_files/S8_two_row_polys.dbf'
+        prj_file = 'input_files/S8_two_row_polys.prj'
+        shx_file = 'input_files/S8_two_row_polys.shx'
 
         files= {'fileName': open(csv_path, 'rb'),
                 'shp_file': open(shp_file, 'rb'),
@@ -40,7 +40,7 @@ def test_insert_sites(self):
 
     def test_insert_citations(self):
         csv_filename = 'citations.csv'
-        csv_path = '../input_files/citations.csv'
+        csv_path = 'input_files/citations.csv'
         files = {'fileName': open(csv_path, 'rb')}
         response = requests.post(
             'http://0.0.0.0:6001/citations?username=guestuser', files=files)
@@ -49,7 +49,7 @@ def test_insert_citations(self):
 
     def test_insert_treatments(self):
         csv_filename = 'treatments.csv'
-        csv = '../input_files/'+csv_filename
+        csv = 'input_files/'+csv_filename
         files = {'fileName': open(csv, 'rb')}
         response = requests.post(
             'http://0.0.0.0:6001/treatments?username=guestuser', files=files)
@@ -58,7 +58,7 @@ def test_insert_treatments(self):
 
     def test_insert_cultivars(self):
         csv_filename = 'cultivars.csv'
-        csv = '../input_files/'+csv_filename
+        csv = 'input_files/'+csv_filename
         files = {'fileName': open(csv, 'rb')}
         response = requests.post(
             'http://0.0.0.0:6001/cultivars', files=files)
@@ -67,7 +67,7 @@ def test_insert_cultivars(self):
 
     def test_insert_experimentSites(self):
         csv_filename = 'experiments_sites.csv'
-        csv = '../input_files/'+csv_filename
+        csv = 'input_files/'+csv_filename
         files = {'fileName': open(csv, 'rb')}
         response = requests.post(
             'http://0.0.0.0:6001/experiments_sites', files=files)
@@ -76,7 +76,7 @@ def test_insert_experimentSites(self):
 
     def test_insert_experimentTreatments(self):
         csv_filename = 'experiments_treatments.csv'
-        csv = '../input_files/'+csv_filename
+        csv = 'input_files/'+csv_filename
         files = {'fileName': open(csv, 'rb')}
         response = requests.post(
             'http://0.0.0.0:6001/experiments_treatments', files=files)
@@ -85,7 +85,7 @@ def test_insert_experimentTreatments(self):
 
     def test_insert_sitesCultivars(self):
         csv_filename = 'sites_cultivars.csv'
-        csv = '../input_files/'+csv_filename
+        csv = 'input_files/'+csv_filename
         files = {'fileName': open(csv, 'rb')}
         response = requests.post(
             'http://0.0.0.0:6001/sites_cultivars', files=files)
@@ -94,7 +94,7 @@ def test_insert_sitesCultivars(self):
 
     def test_insert_citationsSites(self):
         csv_filename = 'citations_sites.csv'
-        csv = '../input_files/'+csv_filename
+        csv = 'input_files/'+csv_filename
         files = {'fileName': open(csv, 'rb')}
         response = requests.post(
             'http://0.0.0.0:6001/citations_sites', files=files)