Merge pull request #2278 from antgonza/redbiom-install

Redbiom install

Author: josenavas

.travis.yml

@@ -1,6 +1,6 @@
 dist: precise
 language: python
-sudo: false
+sudo: required
 env:
   global:
     - PYTHON_VERSION=2.7
@@ -10,6 +10,7 @@ env:
     - TEST_ADD_STUDIES=True COVER_PACKAGE="qiita_core qiita_ware"
 before_install:
   - redis-server --version
+  - sudo -H -u redis redis-server /etc/redis/redis.conf --port 7777 &
   - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
@@ -27,17 +28,32 @@ install:
   # install a few of the dependencies that pip would otherwise try to install
   # when intalling scikit-bio
   - travis_retry conda create --yes -n qiita python=$PYTHON_VERSION pip nose flake8
-    pyzmq networkx pyparsing natsort mock future libgfortran seaborn
+    pyzmq networkx pyparsing natsort mock future libgfortran seaborn nltk
     'pandas>=0.18' 'matplotlib>=1.1.0' 'scipy>0.13.0' 'numpy>=1.7' 'h5py>=2.3.1'
   - source activate qiita
   - pip install -U pip
   - pip install sphinx sphinx-bootstrap-theme nose-timer codecov
-  - travis_retry pip install . --process-dependency-links
   - 'echo "backend: Agg" > matplotlibrc'
+  - git clone https://github.com/nicolasff/webdis
+  - pushd webdis
+  - make
+  - ./webdis &
+  - popd
+  - travis_retry pip install . --process-dependency-links
   # Install the biom plugin so we can run the analysis tests
   - pip install https://github.com/qiita-spots/qiita_client/archive/master.zip
   - pip install https://github.com/qiita-spots/qtp-biom/archive/master.zip --process-dependency-links
   - export QIITA_SERVER_CERT=`pwd`/qiita_core/support_files/server.crt
+  # loading redbiom with Qiita's test set
+  # but first let's make sure redis is empty
+  # following https://github.com/biocore/redbiom/blob/master/Makefile
+  - export REDBIOM_HOST=http://127.0.0.1:7379
+  - curl -s http://127.0.0.1:7379/FLUSHALL > /dev/null
+  - redbiom admin scripts-writable
+  - redbiom admin create-context --name "qiita-test" --description "qiita-test context"
+  - redbiom admin load-sample-metadata --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt
+  - redbiom admin load-sample-metadata-search --metadata `pwd`/qiita_db/support_files/test_data/templates/1_19700101-000000.txt
+  - redbiom admin load-sample-data --table `pwd`/qiita_db/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table.biom --context qiita-test
   - mkdir ~/.qiita_plugins
   - cp $PWD/qiita_core/support_files/BIOM\ type_2.1.4.conf ~/.qiita_plugins
 before_script:

INSTALL.md

@@ -60,6 +60,7 @@ Install the non-python dependencies
 
 * [PostgreSQL](http://www.postgresql.org/download/) (minimum required version 9.3.5, we have tested most extensively with 9.3.6)
 * [redis-server](http://redis.io) (we have tested most extensively with 2.8.17)
+* [webdis] (https://github.com/nicolasff/webdis) (latest version should be fine but we have tested the most with 9ee6fe2 - Feb 6, 2016)
 
 There are several options to install these dependencies depending on your needs:
 
@@ -87,6 +88,27 @@ brew update
 brew install homebrew/versions/redis28
 ```
 
+### webdis
+
+Note that this is the only package that assumes that Qiita is already installed (due to library dependencies). Also, that the general suggestion is to have 2 redis servers running, one for webdis/redbiom and the other for Qiita. The reason for multiple redis servers is so that the redbiom cache can be flushed without impacting the operation of the qiita server itself.
+
+The following instructions install, compile and pre-populates the redbiom redis DB so we assume that redis is running on the default port and that Qiita is fully installed as the redbiom package is installed with Qiita.
+
+```
+git clone https://github.com/nicolasff/webdis
+pushd webdis
+make
+./webdis &
+popd
+# note that this assumes that Qiita is already installed
+fp=`python -c 'import qiita_db; print qiita_db.__file__'`
+qdbd=`dirname $fp`
+redbiom admin scripts-writable
+redbiom admin create-context --name "qiita-test" --description "qiita-test context"
+redbiom admin load-sample-metadata --metadata ${qdbd}/support_files/test_data/templates/1_19700101-000000.txt
+redbiom admin load-sample-metadata-search --metadata ${qdbd}/support_files/test_data/templates/1_19700101-000000.txt
+redbiom admin load-sample-data --table ${qdbd}/support_files/test_data/processed_data/1_study_1001_closed_reference_otu_table.biom --context qiita-test
+```
 
 Install Qiita development version and its python dependencies
 -------------------------------------------------------------
@@ -151,6 +173,13 @@ Next, make a test environment:
 qiita-env make --no-load-ontologies
 ```
 
+Finally, redbiom relies on the REDBIOM_HOST environment variable to set the URL to query. By default is set to Qiita redbiom public repository. To change it you could do:
+
+
+```bash
+export REDBIOM_HOST=http://my_host.com:7379
+```
+
 ## Start Qiita
 
 Start postgres (instructions vary depending on operating system and install method).

qiita_core/support_files/config_test.cfg

@@ -91,7 +91,7 @@ EMAIL = example@domain.com
 # ----------------------------- Redis settings --------------------------------
 [redis]
 HOST = localhost
-PORT = 6379
+PORT = 7777
 PASSWORD =
 # The redis database you will use, redis has a max of 16.
 # Qiita should have its own database

setup.py

@@ -110,9 +110,11 @@
                         'natsort', 'networkx',
                         'scikit-bio == 0.4.2', 'wtforms == 2.0.1',
                         'sphinx-bootstrap-theme', 'Sphinx >= 1.2.2',
-                        'gitpython', 'qiita-files'],
+                        'gitpython', 'qiita-files', 'redbiom'],
       dependency_links=[
         'https://github.com/qiita-spots/qiita-files/archive/master.zip#'
-        'egg=qiita-files-0.1.0-dev'],
+        'egg=qiita-files-0.1.0-dev',
+        'https://github.com/biocore/redbiom/archive/master.zip#'
+        'egg=redbiom-2017.0.1.dev0'],
       classifiers=classifiers
       )