Merge pull request #55 from ola-t/fix_run_filters

fix study filter on runs

.travis.yml

@@ -7,45 +7,28 @@ python:
   - '3.6'
 
 env:
-  - VENV=miniconda
-  - VENV=virtualenv
+  - EMG_CONFIG=$TRAVIS_BUILD_DIR/travis/config.yaml
 
 services:
-  - docker
+  - mysql
   - mongodb
 
 before_install:
-  - pip install "flake8==3.4" pycodestyle pep8-naming
-  - python setup.py sdist
+  - mysql -e 'CREATE DATABASE emg;'
+  - python -V
 
 install:
-  # UnsatisfiableError: The following specifications were found to be in conflict:
-  # - python 3.4*
-  # - urllib3 -> ipaddress -> python 2.7*
-  - if [[ "$VENV" == "miniconda" && "$TRAVIS_PYTHON_VERSION" != "3.4" ]]; then
-      SRCDIR=$(pwd) PYTHON_VERSION=$TRAVIS_PYTHON_VERSION docker/run.sh install;
-    fi
+  - pip install "flake8==3.4" pycodestyle pep8-naming
+  - python setup.py sdist
+  - pip install "git+git://github.com/ola-t/django-rest-framework-json-api@develop#egg=djangorestframework-jsonapi"
 
 before_script:
-  - docker --version
-  # travis by default comes with MySQL 5.5
-  - sudo service mysql stop
-  - docker run --rm --name mysql -p 3306:3306 -e MYSQL_ALLOW_EMPTY_PASSWORD=yes -d mysql:5.6
-  # optional redis
-  # - docker run --rm --name redis -p 6379:6379 -d redis
   - flake8 --version
   - flake8 -v .
-  - mkdir -p ~/emg && cp travis/config.yaml ~/emg/
 
 script:
-  - if [[ "$VENV" == "miniconda" ]]; then
-      SRCDIR=$(pwd) docker/run.sh travis_conda;
-    else
-      SRCDIR=$(pwd) docker/run.sh travis;
-    fi
-
-after_script:
-  - docker stop mysql #redis
+  - pip install -U .
+  - python setup.py test
 
 notifications:
   slack:

README.rst

@@ -20,14 +20,6 @@ Create configuration file in `~/path/to/config.yaml <docker/config.yaml>`_.
 Install
 -------
 
-Install Miniconda::
-
-    wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
-    bash Miniconda3-latest-Linux-x86_64.sh
-
-    export PATH=~/miniconda/bin:$PATH
-
-
 Install application::
 
     pip install "git+git://github.com/ola-t/django-rest-framework-json-api@develop#egg=djangorestframework-jsonapi"

docker/Dockerfile

@@ -6,6 +6,10 @@ RUN yum -y update; yum clean all
 
 RUN yum -y install epel-release gcc bzip2 git wget; yum clean all
 
+RUN yum -y install python34 python34-devel python34-setuptools
+RUN easy_install-3.4 pip
+RUN pip3 install -U pip virtualenv setuptools
+
 # Install mysql tools
 RUN yum -y install mysql mysql-devel
 
@@ -23,4 +27,4 @@ WORKDIR /home/emg
 
 RUN mkdir -p $HOME/emg
 
-ENTRYPOINT ["/tmp/docker/run.sh", "docker"]
+ENTRYPOINT ["/tmp/docker/run.sh"]

docker/docker-compose.yml

@@ -5,7 +5,7 @@ services:
     image: mysql:5.6
     volumes:
       # - ./mysql:/var/lib/mysql:rw
-      - ../database/schema.sql:/docker-entrypoint-initdb.d/schema.sql:ro
+      - ../schema.sql:/docker-entrypoint-initdb.d/schema.sql:ro
     environment:
       - MYSQL_ALLOW_EMPTY_PASSWORD=yes
       - MYSQL_DATABASE=emg
@@ -19,18 +19,19 @@ services:
       - ../docker/config.yaml:/home/emg/emg/config.yaml:ro
     links:
       - mysql
-      - redis
+      - mongodb
     environment:
       - PYTHONUNBUFFERED=0
 
   nginx:
-    image: nginx:1.10
+    image: nginx:1.12
     links:
       - app
     volumes:
-      - ../nginx/conf.d:/etc/nginx/conf.d
+      - ../nginx/conf.d:/etc/nginx/conf.d:ro
+      - ../results:/results:ro
     ports:
       - "80:80"
 
-  redis:
-    image: redis
+  mongodb:
+    image: mongo:3.4

docker/run.sh

@@ -2,102 +2,33 @@
 
 set -eux
 
-entryPoint=${1:-}
 srcDir=${SRCDIR:-"${HOME}/src"}
-condaDir=${CONDADIR:-"${HOME}/miniconda"}
-pythonVer=${PYTHON_VERSION:-"3.6"}
+venvDir=${VENVDIR:-"${HOME}/venv"}
 
-check_conda() {
-  if [[ -f "/etc/profile.d/conda.sh" ]]; then
-    command -v conda >/dev/null && echo "conda detected in $PATH"
-  fi;
-  conda info
-  conda search "^python$"
-}
-
-create_venv() {
-  wget --quiet https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-  /bin/bash miniconda.sh -b -p $condaDir
-  export PATH=$condaDir/bin:$PATH
-  rm -rf miniconda.sh
-  hash -r
-  conda install python=${pythonVer} -y
-  # conda update -q conda
-  conda info -a
-  python -V
-
-  # TODO: wait until 4.4 https://github.com/conda/conda/issues/3200
-  #conda create -q -n test-environment python=$pythonVer
-  #source activate test-environment
-
-}
-
-is_db_running() {
-  local conn=${1:-};
-
-  echo "DB startup..."
-  until mysql $conn -e 'show databases;'; do
-    >&2 echo "MySQL is unavailable - sleeping"
-    sleep 5
-  done
-  >&2 echo "MySQL now accepts connections, creating database..."
-}
-
-install_src() {
-  echo "Installing EMG API..."
-    pip install "git+git://github.com/ola-t/django-rest-framework-json-api@develop#egg=djangorestframework-jsonapi"
-  pip install -U $srcDir
-}
-
-start() {
-  echo "EMG API Start up..."
-
-  # emgcli check --deploy
-  emgcli migrate --fake-initial
-  emgcli collectstatic --noinput
-
-  # development server
-  # emgcli runserver 0.0.0.0:8000
-  emgdeploy -p ${HOME}/emg/emg.pid --bind 0.0.0.0:8000 --workers 5 --reload emgcli.wsgi:application
-
-}
-
-
-# helpers
-install() {
-  create_venv
-  python -V
-}
+rm -f $srcDir/var/django.pid
 
-install_docker() {
-  install
-  pip install -U "django-redis>=4.4"
-  is_db_running "-u root -h mysql -P 3306"
-}
+python3 -V
 
-docker() {
-  install_docker
-  install_src
-  start
-}
+virtualenv -p /usr/bin/python3 $venvDir --system-site-packages
+# $HOME/venv/bin/pip install -U "django-redis>=4.4"
 
-travis() {
-  # Install source, otherwise OSError: [Errno 2] No such file or directory.
-  install_src
-  cd $srcDir
-  python -V
-  python setup.py test
-}
+echo "Installing EMG API..."
+  $venvDir/bin/pip install -U  "git+git://github.com/ola-t/django-rest-framework-json-api@develop#egg=djangorestframework-jsonapi"
+$venvDir/bin/pip install -U $srcDir
 
-travis_conda() {
-  export PATH=$condaDir/bin:$PATH
-  # Install source, otherwise OSError: [Errno 2] No such file or directory.
-  travis
-}
+echo "DB startup..."
+until mysql -u root -h mysql -P 3306 -e 'show databases;'; do
+  >&2 echo "MySQL is unavailable - sleeping"
+  sleep 5
+done
+>&2 echo "MySQL now accepts connections, creating database..."
 
+echo "EMG API Start up..."
 
-rm -f $srcDir/var/django.pid
+# $HOME/venv/bin/emgcli check --deploy
+# $venvDir/bin/emgcli migrate --fake-initial
+$venvDir/bin/emgcli collectstatic --noinput
 
-if [ ! -z ${entryPoint} ] ; then
-  eval $entryPoint
-fi 
+# development server
+# $HOME/venv/bin/emgcli runserver 0.0.0.0:8000
+$venvDir/bin/emgdeploy -p $HOME/emg/emg.pid --bind 0.0.0.0:8000 --workers 5 --reload emgcli.wsgi:application

emgapi/filters.py

@@ -558,7 +558,7 @@ def filter_sample_accession(self, qs, name, value):
         help_text='Study accession')
 
     def filter_study_accession(self, qs, name, value):
-        return qs.filter(sample__studies__accession=value)
+        return qs.filter(study__accession=value)
 
     # include
     include = django_filters.CharFilter(

emgapianns/views.py

@@ -260,9 +260,11 @@ class AnalysisGoTermRelationshipViewSet(  # NOQA
     def get_queryset(self):
         accession = self.kwargs['accession']
         release_version = self.kwargs['release_version']
+        qs = emg_models.AnalysisJob.objects.exclude(
+            experiment_type__experiment_type='amplicon')
         job = get_object_or_404(
-            emg_models.AnalysisJob, accession=accession,
-            pipeline__release_version=release_version
+            qs, accession=accession,
+            pipeline__release_version=release_version,
         )
 
         analysis = None
@@ -297,9 +299,11 @@ class AnalysisGoSlimRelationshipViewSet(  # NOQA
     def get_queryset(self):
         accession = self.kwargs['accession']
         release_version = self.kwargs['release_version']
+        qs = emg_models.AnalysisJob.objects.exclude(
+            experiment_type__experiment_type='amplicon')
         job = get_object_or_404(
-            emg_models.AnalysisJob, accession=accession,
-            pipeline__release_version=release_version
+            qs, accession=accession,
+            pipeline__release_version=release_version,
         )
 
         analysis = None
@@ -334,9 +338,11 @@ class AnalysisInterproIdentifierRelationshipViewSet(  # NOQA
     def get_queryset(self):
         accession = self.kwargs['accession']
         release_version = self.kwargs['release_version']
+        qs = emg_models.AnalysisJob.objects.exclude(
+            experiment_type__experiment_type='amplicon')
         job = get_object_or_404(
-            emg_models.AnalysisJob, accession=accession,
-            pipeline__release_version=release_version
+            qs, accession=accession,
+            pipeline__release_version=release_version,
         )
 
         analysis = None

setup.py

@@ -7,7 +7,7 @@
 _requirements = os.path.join(_base, 'requirements.txt')
 _requirements_test = os.path.join(_base, 'requirements-test.txt')
 
-version = "1.0.6"
+version = "1.0.7"
 
 install_requirements = []
 with open(_requirements) as f: