qiita-spots · antgonza · Jan 13, 2016 · Nov 24, 2015 · Nov 24, 2015 · Nov 24, 2015
diff --git a/.travis.yml b/.travis.yml
@@ -18,7 +18,7 @@ before_install:
   - wget ftp://ftp.microbio.me/pub/qiita/ascp-install-3.5.4.102989-linux-64-qiita.sh -O ascp-install-3.5.4.102989-linux-64-qiita.sh
   - chmod +x ascp-install-3.5.4.102989-linux-64-qiita.sh
   - ./ascp-install-3.5.4.102989-linux-64-qiita.sh
-  - if [ ${TRAVIS_PULL_REQUEST} == "false" ]; then openssl aes-256-cbc -K $encrypted_e698cf0e691c_key -iv $encrypted_e698cf0e691c_iv -in qiita_core/support_files/config_test_travis.cfg.enc -out qiita_core/support_files/config_test_travis.cfg -d; fi
+  - if [ ${TRAVIS_PULL_REQUEST} == "false" ]; then openssl aes-256-cbc -K $encrypted_a2e23aea5f14_key -iv $encrypted_a2e23aea5f14_iv -in qiita_core/support_files/config_test_travis.cfg.enc -out qiita_core/support_files/config_test_travis.cfg -d; fi
 install:
   # install a few of the dependencies that pip would otherwise try to install
   # when intalling scikit-bio
@@ -28,6 +28,9 @@ install:
   - source activate env_name
   - pip install sphinx sphinx-bootstrap-theme coveralls ipython[all]==2.4.1
   - travis_retry pip install .
+  - pushd qiita_plugins/target_gene
+  - travis_retry pip install .
+  - popd
 script:
   - export MOI_CONFIG_FP=`pwd`/qiita_core/support_files/config_test.cfg
   - if [ ${TRAVIS_PULL_REQUEST} == "false" ]; then
@@ -44,7 +47,10 @@ script:
     scripts/qiita-env scripts/qiita-test-install ; fi
   - ls -R /home/travis/miniconda3/envs/env_name/lib/python2.7/site-packages/qiita_pet/support_files/doc/
   - qiita pet webserver
+addons:
+  postgresql: "9.3"
 services:
   - redis-server
+  - postgresql
 after_success:
   - if [ ${TEST_ADD_STUDIES} == "False" ]; then coveralls ; fi
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -6,6 +6,13 @@ Version 0.2.0-dev (Changes since version 0.2.0 go here)
 * Users can now change values and add samples and/or columns to sample and prep templates using the <kbd>Update</kbd> button (see the prep template and sample template tabs).
 * The raw files of a RawData can be now updated using the `qiita db update_raw_data` CLI command.
 * instrument_model is now a required prep template column for EBI submissions.
+* PostgreSQL 9.3.0 is now the minimum required version because we are using the SQL type JSON, included for first time in 9.3.0.
+* The objects `RawData`, `PreprocessedData` and `ProcessedData` have been removed from the system and substituted by a general `Artifact` object.
+* The CLI commands `load_raw`, `load_preprocessed` and `load_processed` have been removed from the system and substituted by `load_artifact`.
+* We incorporated the idea of plugins into the system. Now, all processing could be plugins.
+* QIIME workflows for splitting libraries (SFF/FASTA-QUAL and FASTQ/per-sample-FASTQ) and for picking OTUs has been moved to a new target gene plugin.
+* An initial RESTapi has been introduced as a result of the plugin system, in which OAuth2 authentication is required to access the data.
+* The system has been ported to use HTTPS instead of HTTP.
 
 Version 0.2.0 (2015-08-25)
 --------------------------

diff --git a/INSTALL.md b/INSTALL.md
@@ -6,7 +6,7 @@ Qiita is pip installable, but depends on some non-python packages that must be i
 Install the non-python dependencies
 -----------------------------------
 
-* [PostgreSQL](http://www.postgresql.org/download/) (we have tested most extensively with 9.3)
+* [PostgreSQL](http://www.postgresql.org/download/) (minimum required version 9.3.0, we have tested most extensively with 9.3)
 * [redis-server](http://redis.io) (we have tested most extensively with 2.8.17)
 
 Install both of these packages according to the instructions on their websites.
@@ -30,6 +30,35 @@ pip install https://github.com/biocore/mustached-octo-ironman/archive/master.zip
 pip install qiita-spots
 ```
 
+Install Qiita development version and its python dependencies
+-------------------------------------------------------------
+
+You can also use pip to install the development version of Qiita:
+
+```bash
+pip install numpy
+pip install https://github.com/biocore/mustached-octo-ironman/archive/master.zip --no-deps
+```
+
+Clone the git repository with the development version of Qiita:
+
+```bash
+git clone https://github.com/biocore/qiita.git
+```
+
+Install Qiita:
+```bash
+cd qiita
+pip install .
+```
+
+You will also need to install the target gene plugin for Qiita to be fully functional.
+However, the plugin is already included in the repository so to install it simply execute:
+```bash
+cd qiita_plugins/target_gene
+pip install .
+```
+
 Qiita configuration
 ===================
 After these commands are executed, you will need to:

diff --git a/qiita_core/configuration_manager.py b/qiita_core/configuration_manager.py
@@ -107,6 +107,8 @@ class ConfigurationManager(object):
         The filepath for the configuration file that is loaded
     portal_fp : str
         The filepath to the portal styling config file
+    plugin_launcher : str
+        The script used to start the plugins
     """
     def __init__(self):
         # If conf_fp is None, we default to the test configuration file
@@ -160,6 +162,7 @@ def _get_main(self, config):
         self.max_upload_size = config.getint('main', 'MAX_UPLOAD_SIZE')
         self.require_approval = config.getboolean('main', 'REQUIRE_APPROVAL')
         self.portal = config.get('main', 'PORTAL')
+        self.plugin_launcher = config.get('main', 'PLUGIN_LAUNCHER')
 
         self.valid_upload_extension = [ve.strip() for ve in config.get(
             'main', 'VALID_UPLOAD_EXTENSION').split(',')]
@@ -168,6 +171,15 @@ def _get_main(self, config):
             self.valid_upload_extension = []
             print 'No files will be allowed to be uploaded.'
 
+        self.certificate_file = config.get('main', 'CERTIFICATE_FILE')
+        if not self.certificate_file:
+            self.certificate_file = join(install_dir, 'qiita_core',
+                                         'support_files', 'server.crt')
+        self.key_file = config.get('main', 'KEY_FILE')
+        if not self.key_file:
+            self.key_file = join(install_dir, 'qiita_core', 'support_files',
+                                 'server.key')
+
     def _get_postgres(self, config):
         """Get the configuration of the postgres section"""
         self.user = config.get('postgres', 'USER')

diff --git a/qiita_core/support_files/config_test.cfg b/qiita_core/support_files/config_test.cfg
@@ -22,7 +22,7 @@ LOG_PATH =
 REQUIRE_APPROVAL = True
 
 # Base URL: DO NOT ADD TRAILING SLASH
-BASE_URL = http://localhost
+BASE_URL = https://localhost
 
 # Download path files
 UPLOAD_DATA_DIR = /tmp/
@@ -39,9 +39,16 @@ BASE_DATA_DIR =
 # Valid upload extension, comma separated. Empty for no uploads
 VALID_UPLOAD_EXTENSION = fastq,fastq.gz,txt,tsv,sff,fna,qual
 
-#Portal the site is working under
+# Portal the site is working under
 PORTAL = QIITA
 
+# Script used for launching plugins
+PLUGIN_LAUNCHER = qiita-plugin-launcher
+
+# Webserver certificate file paths
+CERTIFICATE_FILE =
+KEY_FILE =
+
 # ----------------------------- SMTP settings -----------------------------
 [smtp]
 # The hostname to connect to

diff --git a/qiita_core/support_files/config_test_travis.cfg.enc b/qiita_core/support_files/config_test_travis.cfg.enc
diff --git a/qiita_core/support_files/server.crt b/qiita_core/support_files/server.crt
@@ -0,0 +1,20 @@
+-----BEGIN CERTIFICATE-----
+MIIDVjCCAj4CCQCP4XnDqToF2zANBgkqhkiG9w0BAQUFADBtMQswCQYDVQQGEwJV
+UzETMBEGA1UECBMKQ2FsaWZvcm5pYTESMBAGA1UEBxMJU2FuIERpZWdvMQ0wCwYD
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+patQJuxYfOEp9knnBBe+QcaBMY6E7uH6EZz2QwS/gdhfY8e8QXw9sh9ZrQKQlIAK
+Q5l5qxAtek0C90qdseYWoomBhpmqMUicF0OgecbdZ4X6Tfc4hvN5IXUTMn9ZJEaV
+fduah3c7xEkSbHQl6iHnJswNKTc7Amm+BIwuYJjCZxVgKxAgvYzzg/TFU03gqzfE
+h7ARs1p4WdHH+WTMqCZq8+sju3Lum4uwjYaiLaFE7psDkWWAYOu6Jv/o0V1zER/S
+LzNaDfkm5kq4VURhPMQzdAiVdiTNKDFnLB3erg6wG95q5OiGNO1WYSw2
+-----END CERTIFICATE-----
diff --git a/qiita_core/support_files/server.csr b/qiita_core/support_files/server.csr
@@ -0,0 +1,17 @@
+-----BEGIN CERTIFICATE REQUEST-----
+MIICsjCCAZoCAQAwbTELMAkGA1UEBhMCVVMxEzARBgNVBAgTCkNhbGlmb3JuaWEx
+EjAQBgNVBAcTCVNhbiBEaWVnbzENMAsGA1UEChMEVUNTRDESMBAGA1UECxMJS25p
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+kUu++nvrQUvWSsdQzxZq855r2TBA/w==
+-----END CERTIFICATE REQUEST-----
diff --git a/qiita_core/support_files/server.key b/qiita_core/support_files/server.key
@@ -0,0 +1,27 @@
+-----BEGIN RSA PRIVATE KEY-----
+MIIEogIBAAKCAQEAt1ggW4M/l3Wpru4+2CronnqaUWD0ImLnkdAbmDjhGiCdKqdb
+8yzLeKipGaRY383gd5vMWHsKB1I3t+EzFWiYfxd12Evx6MUIXVZSkdConk+8xlmJ
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+UgtsatiprRqzpYQItbPCYyPmDAscA+jsdoZzbXFjlOYz/9BZRCc=
+-----END RSA PRIVATE KEY-----
diff --git a/qiita_core/util.py b/qiita_core/util.py
@@ -10,8 +10,7 @@
 from functools import wraps
 
 from qiita_core.qiita_settings import qiita_config
-from qiita_db.sql_connection import SQLConnectionHandler
-from qiita_db.environment_manager import reset_test_database
+import qiita_db as qdb
 
 with standard_library.hooks():
     from email.mime.multipart import MIMEMultipart
@@ -63,7 +62,7 @@ def qiita_test_checker():
     """
     def class_modifier(cls):
         # First, we check that we are not in a production environment
-        conn_handler = SQLConnectionHandler()
+        conn_handler = qdb.sql_connection.SQLConnectionHandler()
         # It is possible that we are connecting to a production database
         test_db = conn_handler.execute_fetchone("SELECT test FROM settings")[0]
         # Or the loaded configuration file belongs to a production environment
@@ -76,9 +75,9 @@ def class_modifier(cls):
         class DecoratedClass(cls):
             def setUp(self):
                 super(DecoratedClass, self).setUp()
-                self.conn_handler = SQLConnectionHandler()
+                self.conn_handler = qdb.sql_connection.SQLConnectionHandler()
 
-            @reset_test_database
+            @qdb.environment_manager.reset_test_database
             def tearDown(self):
                 super(DecoratedClass, self).tearDown()
 

diff --git a/qiita_db/__init__.py b/qiita_db/__init__.py
@@ -6,4 +6,32 @@
 # The full license is in the file LICENSE, distributed with this software.
 # -----------------------------------------------------------------------------
 
+import base
+import util
+import sql_connection
+import metadata_template
+import analysis
+import artifact
+import commands
+import environment_manager
+import exceptions
+import investigation
+import job
+import logger
+import meta_util
+import ontology
+import portal
+import reference
+import search
+import software
+import study
+import user
+import processing_job
+
 __version__ = "0.2.0-dev"
+
+__all__ = ["analysis", "artifact", "base", "commands", "environment_manager",
+           "exceptions", "investigation", "job", "logger", "meta_util",
+           "ontology", "portal", "reference", "search",
+           "software", "sql_connection", "study", "user", "util",
+           "metadata_template", "processing_job"]