clean up the packaging and distribution code

MANIFEST.in

+include README.md
+include jass/swagger/swagger.yaml
+recursive-include jass/static *
+recursive-include celery_files *

README.md

 # JASS
 
-## setup
+## install
 
-The main requirement is **python 3**. To setup the server in a dedicated virtualenv (you need **virtualenv**), please execute the following from the root directory, once you have cloned the repository:
+You need **python3** to install and use JASS.
 
 ```
-virtualenv venv
-. venv/bin/activate
-pip3 install -r requirements.txt
-# you can quit the virtualenv with
-deactivate
+# install
+pip install [TODO upload to pypi]
 ```
 
-## run
+## configure and import data
 
 ```
-# activate the virtualenv
-. venv/bin/activate
-# run the server, [CTRL+C] to quit
-python -m swagger-server
-# you can quit the virtualenv with
-deactivate
+# configure
+export JASS_DATA_DIR=/tmp/JASSDATA
+# import GWAS data into JASS
+python -m jass create_init_table [TODO use IMpG format]
 ```
 
-## browse
-
-### for end users
-
-TODO
-
-### for developers
-
-The Swagger UI is there:
+## run a server
 
 ```
-http://localhost:8080/ui/
+# launch celery to process tasks
+celery -A jass worker
+# launch the web server
+python -m jass serve
 ```
 
-The Swagger definition for this server's API lives here:
+## use JASS on the command line
 
 ```
-http://localhost:8080/swagger.json
+# list available phenotypes on the command line
+python -m jass list-phenotypes
+# compute joint statistics on the command line into an HDF file
+python -m jass create-worktable --phenotypes z_RA_RA z_ReproGen_AME --worktable-path testwt.h5
+# create the global manhattan plot for a joint statistics file
+python -m jass plot-manhattan --worktable-path testwt.h5 --plot-path testgm.png
+# create the quadrant plot for a joint statistics file
+python -m jass plot-quadrant --worktable-path testwt.h5 --plot-path testqd.png
 ```
 
-# tests
-
-To launch the integration tests, use tox:
-```
-sudo pip install tox
-tox
-```

celery_files/default/celeryd

 CELERYD_NODES="worker"
 CELERY_BIN="/opt/jass/venv/bin/celery"
-CELERY_APP="swagger_server.models.project"
+CELERY_APP="jass.models.project"
 CELERYD_CHDIR="/opt/jass"
 CELERYD_OPTS="--time-limit=3000 --concurrency=1 --max-tasks-per-child=1 --executable=/opt/jass/venv/bin/python"
 CELERYD_LOG_FILE="/opt/jass/log/celery%N.log"

jass.wsgi

@@ -5,7 +5,7 @@ activate_this = '/opt/jass/venv/bin/activate_this.py'
 exec(open(activate_this).read(), dict(__file__=activate_this))
 sys.path.insert(0, '/opt/jass')
 
-from swagger_server.server import get_jass_app
+from jass.server import get_jass_app
 
 app = get_jass_app()
 application = app.app

jass/__init__.py

+from celery import Celery
+import jass.models.project
+
+def make_celery(app):
+    celery = Celery(jass.models.project)
+    celery.conf.update(app.config)
+    TaskBase = celery.Task
+    class ContextTask(TaskBase):
+        abstract = True
+        def __call__(self, *args, **kwargs):
+            with app.app_context():
+                return TaskBase.__call__(self, *args, **kwargs)
+    celery.Task = ContextTask
+    return celery
+
+from flask import Flask
+
+flask_app = Flask(__name__)
+celery = make_celery(flask_app)

swagger_server/config.py → jass/config.py

@@ -11,6 +11,6 @@ if 'JASS_HOST' in os.environ:
 if 'JASS_PORT' in os.environ:
     config['PORT'] = os.environ['JASS_PORT']
 if 'JASS_DATA_DIR' in os.environ:
-    config['JASS_DATA_DIR'] = os.environ['JASS_DATA_DIR']
+    config['DATA_DIR'] = os.environ['JASS_DATA_DIR']
 if 'JASS_INITTABLE_CHUNKSIZE' in os.environ:
     config['INITTABLE_CHUNKSIZE'] = int(os.environ['JASS_INITTABLE_CHUNKSIZE'])

swagger_server/controllers/default_controller.py → jass/controllers/default_controller.py

@@ -5,9 +5,9 @@ from six import iteritems
 from flask import send_file, abort
 import connexion
 
-from swagger_server.models.phenotype import Phenotype, get_available_phenotypes
-from swagger_server.models.project import Project, create_project
-from swagger_server.config import config
+from jass.models.phenotype import Phenotype, get_available_phenotypes
+from jass.models.project import Project, create_project
+from jass.config import config
 PHENOTYPES = get_available_phenotypes(os.path.join(config['DATA_DIR'],'initTable.hdf5')) #FIXME part of the config
 
 def phenotypes_get():

swagger_server/encoder.py → jass/encoder.py

 from connexion.apps.flask_app import FlaskJSONEncoder
 #from connexion.decorators import produces
 from six import iteritems
-from swagger_server.models.base_model_ import Model
+from jass.models.base_model_ import Model
 from pandas import isnull
 
 class JSONEncoder(FlaskJSONEncoder):

swagger_server/models/project.py → jass/models/project.py

@@ -12,7 +12,7 @@ from .base_model_ import Model
 from ..util import deserialize_model
 from .phenotype import Phenotype
 from .worktable import create_worktable_file, get_worktable_summary, get_worktable_genomedata, get_worktable_local_manhattan_data, get_worktable_local_heatmap_data, create_global_plot, create_quadrant_plot
-from swagger_server.config import config
+from jass.config import config
 
 app = Celery('tasks', broker='pyamqp://guest@localhost//')