Merge pull request #16 from bioinformatics-ua/imp/improve_code_structure

Imp/improve code structure

.gitignore

@@ -1,4 +1,156 @@
 bower_components/
 node_modules/
+
+# Retrieved from https://github.com/github/gitignore/blob/752b7678db497edb377fa982ded0c70035393794/Python.gitignore
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
 dist/
-*.pyc
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintainted in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

README.md

@@ -1,8 +1,6 @@
 # GeoDropdown
 GeoDropdown makes use of geowebservice to create a multiple drodpdown lists system, which guarantees that users will provides well formatted locations, according to ISO-3166.
 
-Live demo: [demo.html](demo.html)
-
 # Hierarchical levels
 There are 7 hierarchical levels, which corresponds to 7 dropdown list:
 
@@ -73,31 +71,52 @@ Portugal (wich is a country) geonameid is 2264397, so you can use the link /geod
 [{"geonameid": 2262961, "fcode": "ADM1", "name": "Distrito de Set\u00c3\u00babal", "adm1": 19}, {"geonameid": 2263478, "fcode": "ADM1", "name": "Distrito de Santar\u00c3\u00a9m", "adm1": 18}, {"geonameid": 2264507, "fcode": "ADM1", "name": "Distrito de Portalegre", "adm1": 16}, {"geonameid": 2267056, "fcode": "ADM1", "name": "Distrito de Lisboa", "adm1": 14}, {"geonameid": 2267094, "fcode": "ADM1", "name": "Distrito de Leiria", "adm1": 13}, {"geonameid": 2268337, "fcode": "ADM1", "name": "Distrito de Faro", "adm1": 9}, {"geonameid": 2268404, "fcode": "ADM1", "name": "Distrito de \u00c3\u2030vora", "adm1": 8}, {"geonameid": 2269513, "fcode": "ADM1", "name": "Distrito de Castelo Branco", "adm1": 6}, {"geonameid": 2270984, "fcode": "ADM1", "name": "Distrito de Beja", "adm1": 3}, {"geonameid": 2593105, "fcode": "ADM1", "name": "Madeira", "adm1": 10}, {"geonameid": 2732264, "fcode": "ADM1", "name": "Distrito de Viseu", "adm1": 22}, {"geonameid": 2732437, "fcode": "ADM1", "name": "Distrito de Vila Real", "adm1": 21}, {"geonameid": 2732772, "fcode": "ADM1", "name": "Distrito de Viana do Castelo", "adm1": 20}, {"geonameid": 2735941, "fcode": "ADM1", "name": "Distrito do Porto", "adm1": 17}, {"geonameid": 2738782, "fcode": "ADM1", "name": "Distrito da Guarda", "adm1": 11}, {"geonameid": 2740636, "fcode": "ADM1", "name": "Distrito de Coimbra", "adm1": 7}, {"geonameid": 2742026, "fcode": "ADM1", "name": "Distrito de Bragan\u00c3\u00a7a", "adm1": 5}, {"geonameid": 2742031, "fcode": "ADM1", "name": "Distrito de Braga", "adm1": 4}, {"geonameid": 2742610, "fcode": "ADM1", "name": "Distrito de Aveiro", "adm1": 2}]
 ```
 
-# Server Side:
-# How to make it run
-There is a docker file to run this application. Therefore, if you want to run geodropdown, just go to geowebservice folder and run the following commands:
+# Setup demo
+## Front end:
+```sh
+npm install -g grunt bower serve
+
+# download external dependencies
+bower install
+
+# build dist files
+grunt
+
+# start a dev server to test demo.html
+serve
+```
+
+## Server Side:
+### How to make it run
+There is a docker-compose file to run this application. Therefore, if you want to run geodropdown, just go to geowebservice folder and run the following commands:
 ```
-sh build.sh
-docker-compose up
+cd geowebservice
+docker-compose build
+./start.sh
 ```
 
-Now, you need to have data related to all locations around the world
+### How to load data to the Web Service databases
+
+**Note:** Data is automatically loaded with the start.sh script. You can ignore this section.
 
-# How to load data to the Web Service databases
 To load all the required data, you will need two files from geonames: allCountries.txt and countryInfo.txt.
 You can find them here: [files link](http://download.geonames.org/export/dump/)
 
 The next step is to give the location of those files to the webservice. So you need to change the paths in geowebservice/geodatabase/services.py file, lines 178 and 179.
 
 Now you are prepared to load all locations, simply execute python services.py in console.
 
+## Test it
+Go to [http://localhost:3000/demo](http://localhost:3000/demo)
+
 # Authors:
 
 - Leonardo Coelho	- <[email protected]>
 
 # Contributors
 - Renato Pinho 
 - Luis A. Bastião Silva - <[email protected]>
+- André Pedrosa - <[email protected]>
 
 
 # Mantainers 

geowebservice/.dockerignore

@@ -0,0 +1,4 @@
+Dockerfile
+docker-compose.yml
+venv
+db.sqlite3

geowebservice/Dockerfile

@@ -1,20 +1,12 @@
-FROM debian:jessie
-MAINTAINER Matt Bentley <[email protected]>
+FROM python:3.10
 
-RUN (apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential git python python-dev python-setuptools nginx sqlite3 supervisor)
-RUN (easy_install pip &&\
-  pip install uwsgi)
+WORKDIR /app
 
-ADD requirements.txt /opt/django/app/requirements.txt
-RUN pip install -r /opt/django/app/requirements.txt
-ADD . /opt/django/
+COPY requirements.txt .
+RUN pip install -r requirements.txt
 
-RUN (echo "daemon off;" >> /etc/nginx/nginx.conf &&\
-  rm /etc/nginx/sites-enabled/default &&\
-  ln -s /opt/django/django.conf /etc/nginx/sites-enabled/ &&\
-  ln -s /opt/django/supervisord.conf /etc/supervisor/conf.d/)
+COPY . .
 
-RUN chmod +x /opt/django/run.sh 
-VOLUME ["/opt/django/app"]
-EXPOSE 80
-CMD ["/opt/django/run.sh"]
+EXPOSE 8000
+
+ENTRYPOINT ["gunicorn", "-b 0.0.0.0:8000", "geowebservice.wsgi"]

geowebservice/docker-compose.yml

@@ -1,17 +1,18 @@
-solr:
-    image: solr:5.5.3
-    hostname: solr
-    ports:
-        - "8887:8983"
-
+version: "3"
 
+services:
+  solr:
+    image: solr:5.5.3
+    volumes:
+      - geodata:/opt/solr/server/solr
 
-geodropdownservice:
-    image: bioinformaticsua/geodropdownservice
+  geodropdownservice:
+    build:
+      context: .
     ports:
-        - "8886:80"
-    volumes:
-        - .:/opt/django/app
-    links:
-        - solr:solr
-        
+      - "8886:8000"
+    depends_on:
+      - solr
+
+volumes:
+  geodata:

geowebservice/geodatabase/management/commands/load_data.py

@@ -1,35 +1,25 @@
 # -*- coding: utf-8 -*-
-from __future__ import print_function
-import pysolr
-
-from django.core.management.base import BaseCommand, CommandError
+import logging
 
-import ast
-from django.conf import settings
+from django.core.management.base import BaseCommand
 
 from geodatabase.services import ServiceSolr
 
-import logging
 logger = logging.getLogger()
 logging.basicConfig(level=logging.DEBUG)
 
+
 class Command(BaseCommand):
     help = 'Closes the specified poll for voting'
 
     def add_arguments(self, parser):
-        parser.add_argument('all', nargs='+', type=str)
-        parser.add_argument('countries', nargs='+', type=str)
+        parser.add_argument('countries', type=str)
+        parser.add_argument('all', type=str)
 
     def handle(self, *args, **options):
-        all_locations = ''
-        countries_names = ''
-        try:
-            all_locations = options['all'][0]
-            countries_names = options['countries'][0]
-        except:
-            all_locations = '/home/leonardo/Área de Trabalho/geonames_files/allCountries.txt'
-            countries_names = '/home/leonardo/Área de Trabalho/geonames_files/country.csv'
-
+        countries_names = options['countries']
+        all_locations = options['all']
+
         s = ServiceSolr()
-        s.load_contry_info(countries_names)
-        s.load_initial_data(all_locations)
+        s.load_country_info(countries_names)
+        s.load_initial_data(all_locations)