Merge pull request #36 from qbicsoftware/release/1.0.0

Release 1.0.0

.gitignore

@@ -10,4 +10,14 @@ out/
 *.iws
 .project
 .settings
-.classpath
+.classpath
+
+# VS code
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+
+# Sphinx documentation
+docs/build/

.travis.settings.xml

@@ -0,0 +1,14 @@
+<settings>
+    <servers>
+        <server>
+            <id>nexus-snapshots</id>
+            <username>${env.MAVEN_REPO_USERNAME}</username>
+            <password>${env.MAVEN_REPO_PASSWORD}</password>
+        </server>
+        <server>
+            <id>nexus-releases</id>
+            <username>${env.MAVEN_REPO_USERNAME}</username>
+            <password>${env.MAVEN_REPO_PASSWORD}</password>
+        </server>
+    </servers>
+</settings>

.travis.yml

@@ -0,0 +1,53 @@
+dist: xenial
+language: java
+jdk:
+- openjdk8
+
+sudo: required
+services:
+  - docker
+
+cache:
+  directories:
+  - "$HOME/.m2/repository"
+branches:
+  only:
+  - master
+  - development
+  - "/^[vV]?\\d+\\.\\d+\\.\\d+$/"
+before_install: unset _JAVA_OPTIONS
+script: mvn --quiet -X --activate-profiles !development-build,!release-build --settings
+  .travis.settings.xml clean package
+after_success:
+- bash <(curl -s https://codecov.io/bash)
+deploy:
+- skip_cleanup: true
+  provider: script
+  script: mvn --quiet --activate-profiles development-build,!release-build --settings
+    .travis.settings.xml deploy -DskipITs
+  on:
+    branch: development
+    condition: '"$TRAVIS_EVENT_TYPE" = "push"'
+- skip_cleanup: true
+  provider: script
+  script: mvn --quiet --activate-profiles !development-build,release-build --settings
+    .travis.settings.xml deploy -DskipITs
+  on:
+    condition: '"$TRAVIS_EVENT_TYPE" = "push"'
+    tags: true
+after_deploy:
+- mvn --quiet --activate-profiles !development-build,!release-build --settings .travis.settings.xml
+  site
+notifications:
+  email:
+    on_success: never
+    on_failure: never
+  slack:
+    on_success: never
+    on_failure: always
+    rooms:
+    - secure: "***"
+env:
+  global:
+  - secure: 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
+  - secure: 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

AUTHORS

@@ -0,0 +1,10 @@
+/**
+ * --------------------------------------------------------------------------
+ *                                 meDICit
+ * --------------------------------------------------------------------------
+ *
+ * The following people contributed to Variantstore. 
+ * - Christopher Mohr
+ * - Lukas Heumos
+ * - Sven Fillinger
+ */

CHANGELOG.md

@@ -0,0 +1,15 @@
+# Variantstore: Changelog
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
+and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+
+## v1.0.0 - Valmart - 2021-03-02
+
+Initial release of Variantstore.
+
+### `Main features`
+
+- Store genomic variants with associated metadata
+- Import genomic variants in Variant Call Format
+- Export genomic variants from the store in JSON, FHIRT, and Variant Call Format
+- Query the store for genomic variants and metadata through defined REST entdpoints

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2020 University of Tübingen, Christopher Mohr
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.rst

@@ -0,0 +1,51 @@
+
+.. image:: https://travis-ci.com/qbicsoftware/variantstore-service.svg
+    :target: https://travis-ci.com/qbicsoftware/variantstore-service
+    :alt: Travis Build Status
+
+.. image:: https://readthedocs.org/projects/oncostore-proto-project/badge/?version=latest
+    :target: https://oncostore-proto-project.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+Variantstore
+============
+The **Variantstore** is a Java/Groovy-based service application implemented using the `Micronaut framework <https://micronaut.io>`_ and enables storage and access to information on genomic variants and metadata from a connected database *via* a RESTful API. 
+
+
+Features
+--------
+- Import metadata (JSON files using this `schema <https://github.com/qbicsoftware/mtb-metadata-specs/blob/master/schemes/mtb/variants.metadata.schema.json>`_)
+- Import variants (VCF files, annotated using `SnpEff <http://snpeff.sourceforge.net>`_ or `VEP <https://www.ensembl.org/info/docs/tools/vep/index.html>`_)
+- Import gene information (Ensembl, GFF3 files)  
+- Query information on variants, genes, and cases via (secured) REST endpoints
+- Ask Beacon endpoint if a specific variant exists in the store
+- Export variants in Variant Call Format (VCF) and `FHIR <https://www.hl7.org/fhir/>`_
+
+
+Documentation
+-------------
+Please visit the `Documentation <https://oncostore-proto-project.readthedocs.io/en/latest/>`_ for detailed installation, run and configuration instructions.
+
+Detailed documentation of the RESTful API is additionally available on `SwaggerHub <https://app.swaggerhub.com/apis/christopher-mohr/variantstore/0.6>`_.
+
+
+Database
+--------
+In the current version, the **Variantstore** service can be used with a MariaDB database. If you want to use a different DBMS,
+make sure to specify the database model, set up the datasource in the ``application.yml``, and provide an implementation for the ``VariantstoreStorage`` interface.
+
+We are currently working on the support of `PostgreSQL <https://www.postgresql.org/>`_. 
+
+Contribute
+----------
+The contribution guidelines can be found on `Contributing <https://oncostore-proto-project.readthedocs.io/en/latest/contributing.html>`_.
+
+
+Credits
+-------
+The Variantstore was created within the `DIFUTURE <https://difuture.de>`_ (Data Integration for Future Medicine) Consortium.
+
+This service was designed by `Christopher Mohr <https://github.com/christopher-mohr>`_ and implemented by `Christopher Mohr <https://github.com/christopher-mohr>`_ and `Lukas Heumos <https://github.com/zethson>`_.
+For a full list of authors, please refer to the file `AUTHORS <https://github.com/qbicsoftware/variantstore-service/blob/master/AUTHORS>`_.
+
+Feel free to contribute!

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line.
+SPHINXOPTS    =
+SPHINXBUILD   = sphinx-build
+SPHINXPROJ    = spark-service
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/source/authors.rst

@@ -0,0 +1,7 @@
+Authors
+=======
+
+Variantstore service was designed by `Christopher Mohr <https://github.com/christopher-mohr>`_ and implemented by `Christopher Mohr <https://github.com/christopher-mohr>`_ and `Lukas Heumos <https://github.com/zethson>`_.
+
+For a complete list of authors please refer to `AUTHORS <https://github.com/qbicsoftware/variantstore-service/blob/master/AUTHORS>`_. 
+