Initial commit

Note that this commit ports over the contents of the previously existing
repository.

Fixes qiita-spots#59

.coveragerc

@@ -0,0 +1,19 @@
+# this file is based on the examples provided on scikit-learn's .coveragerc
+
+[run]
+omit =
+    */test*
+    */__init__.py
+source = qiita_core,qiita_ware,qiita_db,qiita_pet 
+branch = True
+include = */qiita_*/*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    def __repr__
+    raise NotImplementedError
+    if __name__ == .__main__.:
+omit =
+    */test*
+    */__init__.py

.gitignore

@@ -0,0 +1,46 @@
+*.py[cod]
+
+# C extensions
+*.so
+
+# Packages
+*.egg
+*.egg-info
+dist
+build
+eggs
+parts
+bin
+var
+sdist
+develop-eggs
+.installed.cfg
+lib
+lib64
+
+# Installer logs
+pip-log.txt
+
+# Unit test / coverage reports
+.coverage
+.tox
+nosetests.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Config files
+config.py
+
+# OSX files
+.DS_Store
+
+# vi swap and temp files
+*.swp
+*.swo
+*~

.travis.yml

@@ -0,0 +1,34 @@
+language: python
+env:
+  - PYTHON_VERSION=3.4
+  - PYTHON_VERSION=2.7
+before_install:
+  - wget http://repo.continuum.io/miniconda/Miniconda-2.2.2-Linux-x86_64.sh -O miniconda.sh
+  - chmod +x miniconda.sh
+  - ./miniconda.sh -b
+  - export PATH=/home/travis/anaconda/bin:$PATH
+  # Update conda itself
+  - conda update --yes conda
+install:
+  - conda create --yes -n env_name python=$PYTHON_VERSION pip nose pep8 openpyxl=1.8.2 pandas ipython pyzmq
+  - source activate env_name
+  - pip 
+  - pip install coveralls
+  - pip install .
+script:
+  - ipython profile create qiita_general --parallel
+  - ipython profile create qiita_demo --parallel
+  - ipython profile create qiita_reserved --parallel
+  - qiita_env start_cluster --cluster general
+  - qiita_env start_cluster --cluster demo
+  - qiita_env start_cluster --cluster reserved
+  - qiita_env make_env --env test
+  - nosetests --with-doctest --with-coverage
+  - pep8 qiita_db qiita_core qiita_pet setup.py
+  # we need to run the test suite from setup.py for coveralls to grab the info
+  # - coverage run setup.py test
+  # - coverage report -m
+services:
+  - redis-server
+after_success:
+  - coveralls

INSTALL.md

@@ -0,0 +1,54 @@
+Dependencies
+------------
+
+Qiita is a python package, with support for python 2.7 and 3.2, that depends on the following python libraries (all of them can be installed using pip):
+
+<!--
+* [pgbouncer](http://pgfoundry.org/projects/pgbouncer)
+* [IPython](https://github.com/ipython/ipython)
+-->
+
+* [tornado 3.1.1](http://www.tornadoweb.org/en/stable/)
+* [tornado-redis](https://pypi.python.org/pypi/tornado-redis)
+* [Psycopg2](http://initd.org/psycopg/download/)
+* [click](http://click.pocoo.org/)
+* [NumPy](https://github.com/numpy/numpy)
+* [Pandas](http://pandas.pydata.org/)
+* [QIIME development version](https://github.com/biocore/qiime)
+* [future](http://python-future.org/)
+* [bcrypt](https://github.com/pyca/bcrypt/)
+* [redis](https://github.com/andymccurdy/redis-py)
+
+And on the following packages:
+
+* [PostgresSQL 9.3](http://www.postgresql.org/download/)
+* [redis 2.8.0](https://pypi.python.org/pypi/redis/)
+
+<!--
+* [redis-server](http://redis.io)
+-->
+
+Install
+-------
+
+Once you have [PostgresSQL](http://www.postgresql.org/download/) and [redis](https://pypi.python.org/pypi/redis/) installed (follow the instruction on their web site), simply run these commands to install qiita and configure the demo environment, replacing $QIITA_DIR for the path where qiita is installed
+(note that if you are not using Ubuntu you might need to follow the instructions in the next section):
+
+```bash
+echo "export QIITA_CONFIG_FP=$QIITA_DIR/qiita_core/support_files/config_demo.txt" >> ~/.bashrc
+source ~/.bashrc
+pip install https://github.com/biocore/qiita/archive/master.zip
+qiita_env make_env --env demo
+```
+## If using other operating systems that are not Ubuntu
+
+You will need to add the postgres user to the database. In order to do this, run:
+
+```bash
+createuser -s postgres -d
+```
+
+If you receive the following error, you can ignore this step and continue with the qiita installation:
+```bash
+createuser: creation of new role failed: ERROR:  role "postgres" already exists
+```

LICENSE

@@ -0,0 +1,27 @@
+Copyright (c) 2013, Qiita development team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+  Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+  Redistributions in binary form must reproduce the above copyright notice, this
+  list of conditions and the following disclaimer in the documentation and/or
+  other materials provided with the distribution.
+
+  Neither the name of the {organization} nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -0,0 +1,14 @@
+include README.md
+include INSTALL.md
+include LICENSE
+
+graft qiita_core
+graft qiita_db
+graft qiita_pet
+graft qitta_ware
+graft scripts
+
+global-exclude *.pyc
+global-exclude *.pyo
+global-exclude .git
+global-exclude *~

README.md

@@ -0,0 +1,7 @@
+Qiita
+=====
+
+[![Build Status](https://travis-ci.org/biocore/qiita.png?branch=master)](https://travis-ci.org/biocore/qiita)
+[![Coverage Status](https://coveralls.io/repos/biocore/qiita/badge.png?branch=master)](https://coveralls.io/r/biocore/qiita)
+
+Welcome to Qiita (canonically pronounced *cheetah*) the QIIME databasing effort to enable rapid analysis of microbial ecology datasets. The Qiita repository is responsible for defining the data model and the Python API for interacting with a Qiita database.

config/database.yml

@@ -0,0 +1,4 @@
+test:
+  adapter: postgresql
+  database: qiita_test
+  username: postgres

qiita_core/__init__.py

@@ -0,0 +1,10 @@
+#!/usr/bin/env python
+from __future__ import division
+
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------

qiita_core/configuration_manager.py

@@ -0,0 +1,119 @@
+# -----------------------------------------------------------------------------
+# Copyright (c) 2014--, The Qiita Development Team.
+#
+# Distributed under the terms of the BSD 3-clause License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# -----------------------------------------------------------------------------
+
+from functools import partial
+from os.path import join, dirname, abspath
+from os import environ
+from future import standard_library
+with standard_library.hooks():
+    from configparser import (ConfigParser, NoOptionError,
+                              MissingSectionHeaderError)
+
+
+class ConfigurationManager(object):
+    """Holds the QIITA configuration
+
+    Parameters
+    ----------
+    conf_fp: str, optional
+        Filepath to the configuration file. Default: config_test.txt
+
+    Attributes
+    ----------
+    test_environment : bool
+        If true, we are in a test environment.
+    base_data_dir : str
+        Path to the base directorys where all data file are stored
+    user : str
+        The postgres user
+    password : str
+        The postgres password for the previous user
+    database : str
+        The postgres database to connect to
+    host : str
+        The host where the database lives
+    port : int
+        The port used to connect to the postgres database in the previous host
+    ipyc_demo : str
+        The IPython demo cluster profile
+    ipyc_demo_n : int
+        The size of the demo cluster
+    ipyc_reserved : str
+        The IPython reserved cluster profile
+    ipyc_reserved_n : int
+        The size of the reserved cluster
+    ipyc_general : str
+        The IPython general cluster profile
+    ipyc_general_n : int
+        The size of the general cluster
+    """
+    def __init__(self):
+        # If conf_fp is None, we default to the test configuration file
+        try:
+            conf_fp = environ['QIITA_CONFIG_FP']
+        except KeyError:
+            conf_fp = join(dirname(abspath(__file__)),
+                           'support_files/config_test.txt')
+
+        # Parse the configuration file
+        config = ConfigParser()
+        with open(conf_fp, 'U') as conf_file:
+            config.readfp(conf_file)
+
+        _expected_sections = set(['main', 'ipython', 'redis', 'postgres'])
+        if set(config.sections()) != _expected_sections:
+            missing = _expected_sections - set(config.sections())
+            raise MissingSectionHeaderError("Missing: %r" % missing)
+
+        self._get_main(config)
+        self._get_postgres(config)
+        self._get_redis(config)
+        self._get_ipython(config)
+
+    def _get_main(self, config):
+        """Get the configuration of the main section"""
+        self.test_environment = config.getboolean('main', 'TEST_ENVIRONMENT')
+        try:
+            self.base_data_dir = config.get('main', 'BASE_DATA_DIR')
+        except NoOptionError as e:
+            if self.test_environment:
+                self.base_data_dir = join(dirname(abspath(__file__)),
+                                          '../test_data')
+            else:
+                raise e
+
+    def _get_postgres(self, config):
+        """Get the configuration of the postgres section"""
+        self.user = config.get('postgres', 'USER')
+        try:
+            self.password = config.get('postgres', 'PASSWORD')
+        except NoOptionError as e:
+            if self.test_environment:
+                self.password = None
+            else:
+                raise e
+        self.database = config.get('postgres', 'DATABASE')
+        self.host = config.get('postgres', 'HOST')
+        self.port = config.getint('postgres', 'PORT')
+
+    def _get_redis(self, config):
+        """Get the configuration of the redis section"""
+        pass
+
+    def _get_ipython(self, config):
+        """Get the configuration of the ipython section"""
+        sec_get = partial(config.get, 'ipython')
+        sec_getint = partial(config.getint, 'ipython')
+
+        self.ipyc_demo = sec_get('DEMO_CLUSTER')
+        self.ipyc_reserved = sec_get('RESERVED_CLUSTER')
+        self.ipyc_general = sec_get('GENERAL_CLUSTER')
+
+        self.ipyc_demo_n = sec_getint('DEMO_CLUSTER_SIZE')
+        self.ipyc_reserved_n = sec_getint('RESERVED_CLUSTER_SIZE')
+        self.ipyc_general_n = sec_getint('GENERAL_CLUSTER_SIZE')

qiita_core/environment_manager.py

@@ -0,0 +1,16 @@
+from IPython.parallel.apps.ipclusterapp import IPClusterStart, IPClusterStop
+
+
+def start_cluster(profile, n):
+    """Start a cluster"""
+    c = IPClusterStart(profile=profile, log_level=0, daemonize=True)
+    c.n = n
+    c.initialize(argv=[])
+    c.start()
+
+
+def stop_cluster(profile):
+    """Stop a cluster"""
+    c = IPClusterStop(profile=profile, log_level=0)
+    c.initialize(argv=[])
+    c.start()