Merge pull request #29 from Ensembl/features/es-connexion

Features/es connexion

.travis.yml

@@ -14,6 +14,8 @@ env:
   ES_INDEX: "datacheck_results"
   ES_PORT: "9200"
   ES_HOST: "localhost"
+  ES_USER: ""
+  ES_PASSWORD: ""
 
 before_install:
   - sudo rm /usr/local/bin/docker-compose
@@ -23,8 +25,7 @@ before_install:
 
 before_script:
   - docker-compose -f src/tests/docker-compose.yml  up -d
-  - pip install -r requirements.txt
-  - pip install coverage
+  - pip install -r requirements-test.txt
   - pip install .
 
 script:

Dockerfile

@@ -12,11 +12,12 @@ COPY --chown=appuser:appuser . /home/appuser/datachecks
 #Install dependencies
 RUN python -m venv /home/appuser/datachecks/venv
 ENV PATH="/home/appuser/datachecks/venv/bin:$PATH"
-RUN pip install -r requirements.txt
+RUN pip install wheel
+RUN pip install --upgrade pip
 RUN pip install .
 # clone datacheck app
 ENV DATACHECK_CONFIG_PATH="/home/appuser/datachecks/config.yaml"
 RUN git clone https://github.com/Ensembl/ensembl-datacheck.git
 
 EXPOSE 5001
-CMD  ["gunicorn", "--config", "/home/appuser/datachecks/gunicorn_config.py", "-b", "0.0.0.0:5001", "ensembl.production.datacheck.app.main:app"]
+CMD  ["gunicorn", "--config", "/home/appuser/datachecks/gunicorn_config.py", "ensembl.production.datacheck.app.main:app"]

MANIFEST.in

@@ -1,6 +1,7 @@
 include LICENSE
 include NOTICE
 include VERSION
+include requirements.txt
 include src/ensembl/production/datacheck/templates/*
 include src/ensembl/production/datacheck/static/js/*
 include src/ensembl/production/datacheck/static/css/*

VERSION

@@ -1 +1 @@
-1.2.2
+2.0.0

gunicorn_config.py

@@ -29,8 +29,9 @@
 #       range.
 #
 
-#  bind = '0.0.0.0:5006'
-backlog = 2048
+import os
+bind = os.getenv("GUNICORN_BIND", "0.0.0.0:5001")
+backlog = int(os.getenv("GUNICORN_BACKLOG", "2048"))
 
 #
 # Worker processes

requirements-test.txt

@@ -0,0 +1,3 @@
+-r requirements.txt
+pytest
+coverage

requirements.in

@@ -1,4 +1,4 @@
-ensembl-prodinf-core~=2.0.0
+ensembl-prodinf-core==2.0.5
 Bootstrap-Flask
 Click
 elasticsearch>=6.8.1,<7.0.0
@@ -12,6 +12,5 @@ mysqlclient
 pytest
 requests
 SQLAlchemy
-sqlalchemy_utils==0.37.0
 wtforms
-ensembl-py@git+https://github.com/Ensembl/ensembl-py.git#egg=ensembl-py
+ensembl-py@git+https://github.com/Ensembl/ensembl-py.git@1.0.0dev2#egg=ensembl-py

requirements.txt

@@ -1,44 +1,44 @@
 #
-# This file is autogenerated by pip-compile with python 3.7
-# To update, run:
+# This file is autogenerated by pip-compile with Python 3.10
+# by the following command:
 #
 #    pip-compile requirements.in
 #
-amqp==5.1.0
+amqp==5.1.1
     # via kombu
-attrs==21.4.0
-    # via
-    #   jsonschema
-    #   pytest
-bootstrap-flask==2.0.2
+attrs==23.1.0
+    # via jsonschema
+bootstrap-flask==2.2.0
     # via -r requirements.in
 certifi==2020.12.5
     # via
     #   ensembl-prodinf-core
     #   requests
-charset-normalizer==2.0.12
+charset-normalizer==3.1.0
     # via requests
-click==8.0.4
+click==8.1.3
     # via
     #   -r requirements.in
     #   flask
 deprecation==2.1.0
     # via ensembl-prodinf-core
-dnspython==2.2.1
+dnspython==2.3.0
     # via email-validator
 elasticsearch==6.8.2
     # via -r requirements.in
-email-validator==1.1.3
+email-validator==2.0.0.post1
     # via -r requirements.in
 ensembl-hive @ git+https://github.com/Ensembl/ensembl-hive.git@main
     # via ensembl-py
-ensembl-prodinf-core==2.0.3
+ensembl-prodinf-core==2.0.5
     # via -r requirements.in
-ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git
+ensembl-py @ git+https://github.com/Ensembl/ensembl-py.git@1.0.0dev2
     # via -r requirements.in
+exceptiongroup==1.1.1
+    # via pytest
 flasgger==0.9.5
     # via -r requirements.in
-flask==2.0.3
+flask==2.2.3
     # via
     #   -r requirements.in
     #   bootstrap-flask
@@ -47,61 +47,48 @@ flask==2.0.3
     #   flask-wtf
 flask-cors==3.0.10
     # via -r requirements.in
-flask-wtf==1.0.0
+flask-wtf==1.1.1
     # via -r requirements.in
-greenlet==1.1.2
+greenlet==2.0.2
     # via sqlalchemy
 gunicorn==20.1.0
     # via -r requirements.in
-idna==3.3
+idna==3.4
     # via
     #   email-validator
     #   requests
-importlib-metadata==4.11.3
-    # via
-    #   click
-    #   jsonschema
-    #   kombu
-    #   pluggy
-    #   pytest
-    #   sqlalchemy
-importlib-resources==5.4.0
-    # via jsonschema
-iniconfig==1.1.1
+iniconfig==2.0.0
     # via pytest
-itsdangerous==2.1.1
+itsdangerous==2.1.2
     # via
     #   flask
     #   flask-wtf
-jinja2==3.0.3
+jinja2==3.1.2
     # via flask
-jsonschema==4.4.0
+jsonschema==4.17.3
     # via flasgger
 kombu==5.0.2
     # via ensembl-prodinf-core
-markupsafe==2.1.1
+markupsafe==2.1.2
     # via
     #   jinja2
+    #   werkzeug
     #   wtforms
-mistune==2.0.2
+mistune==2.0.5
     # via flasgger
-mysqlclient==2.1.0
+mysqlclient==2.1.1
     # via
     #   -r requirements.in
     #   ensembl-py
-packaging==21.3
+packaging==23.1
     # via
     #   deprecation
     #   pytest
 pluggy==1.0.0
     # via pytest
-py==1.11.0
-    # via pytest
-pyparsing==3.0.7
-    # via packaging
-pyrsistent==0.18.1
+pyrsistent==0.19.3
     # via jsonschema
-pytest==7.1.1
+pytest==7.3.1
     # via
     #   -r requirements.in
     #   ensembl-py
@@ -115,7 +102,7 @@ pyyaml==6.0
     #   ensembl-prodinf-core
     #   ensembl-py
     #   flasgger
-requests==2.27.1
+requests==2.28.2
     # via
     #   -r requirements.in
     #   ensembl-prodinf-core
@@ -125,41 +112,31 @@ six==1.15.0
     #   ensembl-prodinf-core
     #   flasgger
     #   flask-cors
-    #   sqlalchemy-utils
-sqlalchemy==1.4.32
+sqlalchemy==1.4.47
     # via
     #   -r requirements.in
     #   ensembl-prodinf-core
     #   ensembl-py
     #   sqlalchemy-utils
-sqlalchemy-utils==0.37.0
+sqlalchemy-utils==0.38.3
     # via
-    #   -r requirements.in
     #   ensembl-prodinf-core
     #   ensembl-py
 tomli==2.0.1
     # via pytest
-typing-extensions==4.1.1
-    # via
-    #   importlib-metadata
-    #   jsonschema
-urllib3==1.26.9
+urllib3==1.26.15
     # via
     #   elasticsearch
     #   requests
 vine==5.0.0
     # via amqp
-werkzeug==2.0.3
+werkzeug==2.2.3
     # via flask
 wtforms==3.0.1
     # via
     #   -r requirements.in
     #   bootstrap-flask
     #   flask-wtf
-zipp==3.7.0
-    # via
-    #   importlib-metadata
-    #   importlib-resources
 
 # The following packages are considered to be unsafe in a requirements file:
 # setuptools

setup.py

@@ -9,10 +9,11 @@
 #    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 #    See the License for the specific language governing permissions and
 #    limitations under the License.
+import os
 from pathlib import Path
 
-from setuptools import setup, find_namespace_packages, find_packages
- 
+from setuptools import setup, find_namespace_packages
+
 with open(Path(__file__).parent / 'README.md') as f:
     readme = f.read()
 with open(Path(__file__).parent / 'VERSION') as f:
@@ -25,14 +26,13 @@ def import_requirements():
         return [line.rstrip() for line in file.readlines()]
 
 
-
 setup(
     name='datacheck',
-    version=version,
+    version=os.getenv('CI_COMMIT_TAG', version),
     namespace_packages=['ensembl'],
     packages=find_namespace_packages(where='src', include=['ensembl.*']),
-    package_dir={'': 'src'}, 
-    include_package_data=True,   
+    package_dir={'': 'src'},
+    include_package_data=True,
     url='https://github.com/Ensembl/ensembl-prodinf-datacheck',
     license='APACHE 2.0',
     author='vinay kaikala',
@@ -41,6 +41,7 @@ def import_requirements():
     maintainer_email='ensembl-production@ebi.ac.uk',
     description='Ensembl datacheck service',
     python_requires='>=3.7',
+    install_requires=import_requirements(),
     classifiers=[
         'Development Status :: 5 - Production/Stable',
         'Intended Audience :: Developers',
@@ -60,4 +61,4 @@ def import_requirements():
             'datacheck_api = ensembl.production.datacheck.runserver:main'
         ]
     }
-)
+)