Features/merge services

.dockerignore

@@ -0,0 +1,162 @@
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+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
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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 maintained 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/
+

.gitignore

@@ -139,3 +139,4 @@ dmypy.json
 
 # Cython debug symbols
 cython_debug/
+.python-version

Dockerfile

@@ -0,0 +1,23 @@
+FROM python:3.8.15-alpine
+# Package
+RUN apk update && apk add --no-cache git mariadb-dev build-base
+
+RUN addgroup -S appgroup && adduser -S appuser -G appgroup
+RUN mkdir -p /usr/src/app
+RUN chown -R appuser:appgroup /usr/src/app/
+
+USER appuser
+WORKDIR /usr/src/app
+ENV PYTHONDONTWRITEBYTECODE 1
+ENV PYTHONUNBUFFERED 1
+ENV PIP_ROOT_USER_ACTION=ignore
+
+COPY --chown=appuser:appgroup . /usr/src/app/
+ENV PATH="/usr/src/app/venv/bin:$PATH"
+
+RUN python -m venv /usr/src/app/venv/
+RUN pip install --upgrade pip
+RUN pip install .
+RUN pip uninstall -y ensembl-hive
+
+CMD ["/usr/src/app/venv/bin/python", "/usr/src/app/src/ensembl/production/metadata/grpc/service.py"]

MANIFEST.in

@@ -1,4 +1,6 @@
 include LICENSE
 include NOTICE
 include VERSION
-recursive-include src/ensembl/production/metadata/api/sample/ *
+recursive-include src/ensembl/production/metadata/api/sample/ *
+include README.md
+include requirements.txt

NOTICE

@@ -1,4 +1,4 @@
-Ensembl Metadata API
+Ensembl Metadata API/Services
 Copyright [2018-2023] EMBL-European Bioinformatics Institute
 
 This product includes software developed at:

README.md

@@ -1,9 +1,10 @@
-# Ensembl Metadata API
+<<<<<<< HEAD
+# Ensembl Metadata API / GRPC API 
+# SQLAlchemy ORM for the Ensembl Metadata database.
+# GRPC Service protofile to interact with metadata database through GRPC
 
 [![Build Status](https://travis-ci.com/Ensembl/ensembl-metadata-api.svg?branch=main)](https://travis-ci.com/Ensembl/ensembl-metadata-api)
 
-SQLAlchemy ORM for the Ensembl Metadata database.
-
 ## System Requirements
 
 - Python 3.8+
@@ -32,10 +33,6 @@ pip install -r requirements.txt
 
 [ensembl-metadata-admin](https://github.com/Ensembl/ensembl-metadata-admin): Django ORM for the Ensembl Metadata database
 
-[ensembl-metadata-registry](https://github.com/Ensembl/ensembl-metadata-registry): GUI for the Ensembl Metadata database
-
-[ensembl-metadata-service](https://github.com/Ensembl/ensembl-metadata-service): gRPC layer for the Ensembl Metadata database
-
 
 ## Development
 
@@ -59,6 +56,24 @@ pip install --upgrade pip
 pip install -r requirements-dev.txt
 ```
 
+=======
+To generate client and server files
+(Remember to run these after adding a new method in ensembl_metadata.proto)
+```
+python3 -m grpc_tools.protoc -Iprotos --python_out=src --grpc_python_out=src protos/ensembl/production/metadata/grpc/ensembl_metadata.proto
+```
+
+Start the server script
+
+```
+PYTHONPATH='src' python3 src/ensembl/production/metadata/grpc/service.py
+```
+
+Start the client script
+```
+PYTHONPATH='src' python3 src/ensembl/production/metadata/grpc/client_examples.py
+```
+
 ### Testing
 
 Run test suite:
@@ -78,6 +93,41 @@ To actually reformat all files contained in `src`:
 ```
 cd ensembl-metadata-api
 black src
+PYTHONPATH='src' pytest
+```
+
+To run tests, calculate and display testing coverage stats:
+```
+cd ensembl-metadata-api
+coverage run -m pytest
+coverage report -m
+```
+
+#### Explore test DB content
+
+As for now, some of the test DB sqlite content is different from what's in MySQL metadata DB (e.g. release `version` in `ensembl_release`)
+
+> `test.db` created when running tests is deleted once tests are executed.
+
+To take a look at the test data you can create a temporary `sampledb.db` importing `tables.sql` content using the command:
+
+```
+cat tables.sql | sqlite3 sampledb.db
+```
+
+You can then open `sampledb.db` using [DB Browser for SQLite](https://sqlitebrowser.org/dl/).
+
+### Automatic Formatting
+```
+cd ensembl-metadata-api
+black --check src tests
+```
+Use `--diff` to print a diff of what Black would change, without actually changing the files.
+
+To actually reformat all files contained in `src` and `test`:
+```
+cd ensembl-metadata-api
+black src tests
 ```
 
 ### Linting and type checking
@@ -88,3 +138,20 @@ mypy src
 ```
 Pylint will check the code for syntax, name errors and formatting style.
 Mypy will use type hints to statically type check the code.
+=======
+cd ensembl-metadata-service
+pylint src tests
+mypy src tests
+```
+Pylint will check the code for syntax, name errors and formatting style.
+Mypy will use type hints to statically type check the code.
+
+### To build docker image
+```
+docker build -t ensembl-metadata-service .
+```
+
+### To run docker container
+```
+ docker run -t -i -e METADATA_URI=<URI> -e TAXONOMY_URI=<URI> -p 80:80 ensembl-metadata-service
+```

VERSION

@@ -1 +1 @@
-1.3.4
+2.0.0

conftest.py

@@ -10,15 +10,40 @@
 #   See the License for the specific language governing permissions and
 #   limitations under the License.
 import os
-import logging
 from pathlib import Path
 
-import pytest
 from _pytest.config import Config
+import pytest
+import sqlalchemy as db
+
+from ensembl.production.metadata.grpc.adaptors.genome import GenomeAdaptor
+from ensembl.production.metadata.grpc.adaptors.release import ReleaseAdaptor
 
 pytest_plugins = ("ensembl.plugins.pytest_unittest",)
 
 
 def pytest_configure(config: Config) -> None:
     pytest.dbs_dir = Path(__file__).parent / 'src' / 'ensembl' / 'production' / 'metadata' / 'api' / 'sample'
 
+@pytest.fixture(scope="class")
+def engine(multi_dbs):
+    os.environ["METADATA_URI"] = multi_dbs["ensembl_metadata"].dbc.url
+    os.environ["TAXONOMY_URI"] = multi_dbs["ncbi_taxonomy"].dbc.url
+    yield db.create_engine(multi_dbs["ensembl_metadata"].dbc.url)
+
+
+@pytest.fixture(scope="class")
+def genome_db_conn(multi_dbs):
+    genome_conn = GenomeAdaptor(
+        metadata_uri=multi_dbs["ensembl_metadata"].dbc.url,
+        taxonomy_uri=multi_dbs["ncbi_taxonomy"].dbc.url
+    )
+    yield genome_conn
+
+
+@pytest.fixture(scope="class")
+def release_db_conn(multi_dbs):
+    release_conn = ReleaseAdaptor(
+        metadata_uri=multi_dbs["ensembl_metadata"].dbc.url
+    )
+    yield release_conn