Difference between revisions of "GOlr"

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(General notes)
(Readying OWLTools)
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First, we need to download and build OWLTools--it contains the loader code that GO uses for ontology and GAF files, as well as the tools to generate a new Solr schema from AmiGO 2 YAML config files. The code should be self-sufficient and easy to build on a machine with an internet connection.
 
First, we need to download and build OWLTools--it contains the loader code that GO uses for ontology and GAF files, as well as the tools to generate a new Solr schema from AmiGO 2 YAML config files. The code should be self-sufficient and easy to build on a machine with an internet connection.
  
 +
mkdir -p ~/local/src/svn
 
  cd ~/local/src/svn
 
  cd ~/local/src/svn
 
  svn checkout http://owltools.googlecode.com/svn/trunk/ owltools
 
  svn checkout http://owltools.googlecode.com/svn/trunk/ owltools

Revision as of 14:53, 3 April 2013

Overview

This page describes the status of the public Solr index for the GO. This index will replace some of the query functionality for GOOSE as well as become the new backend for AmiGO 2 and other services. A preview server is now active at http://golr.berkeleybop.org.

Public beta

The preview server at http://golr.berkeleybop.org is currently in beta.

Some preview documentation is at http://cdn.berkeleybop.org/jsapi/bbop-js/docs/index.html

Use

Feel free to use it as you will and start to write for it. As this is still a little early, we are only loading the GO, CL, ECO, and taxslim, as well as non-IEA annotations from the GAFs. Please see the AmiGO_Labs caveats, as well as the downtime information on this page.

Implementation progress

We are now loading properly from owltools.

We have looked at nginx as a reverse proxy for speed and to prevent unauthorized access to non-select URLs on the Solr server, and found it to be good.

The GOlr server is now active at http://golr.berkeleybop.org (nginx front on stove).

We now also have http://amigo2.berkeleybop.org working on stove and backed by golr.berkeleybop.org.

We are now on Solr 3.6. At some point we'd like to get on 4.x for some improvements including pivot tables.

Schema progress

We are currently working towards a flexible schema as defined in the owltools code. As we roll it out for the AmiGO backend and as a replacement for common GOOSE queries, we expect to find holes in the schema, documented below.

Currently, the index is entirely populated by through an owltools command line program, using YAML files for configuration. For more information, see the Installation section below.

Rewriting old GOOSE query examples for the new GOlr Schema

Example queries on the wiki.

  • Some old queries require the use of Solr facets and some modification of code Seth has written to present simpler results queries (i.e. the facet results are not displayed).
  • Note: hierarchical queries that 'combine' facet queries can be handled by the facet.pivot functionality that is available in Solr 4. In the meantime, we'll see if we can devise a work-around.

Current holes in the GOlr schema

  • None listed at this time...

Downtime

Now that we have entered beta, downtimes are sporactic as we work with the software stack. As we approach production, the automatic update times will be decided and posted.

Local installation (data and schema development)

These instructions are intended to illustrate how to install the GOlr server software for AmiGO 2 on a Ubuntu 12.04 LTS Desktop. With careful reading, these instructions should be generalizable to other cases.

General notes

The following packages are required:

  • openjdk-6-jdk
  • jetty
  • subversion

Jetty will need to be setup to start and listen to an external address if you want.

Also, you will need a version of Maven 3 (mvn) to use and build OWLTools if you are trying to load data or produce a schema--the one in Ubuntu for 12.04 is stuck at Maven 2 and not compatible. It is a fairly simple process to download it and make sure that it is in your path.

mkdir -p ~/local/src/java
cd ~/local/src/java
wget http://apache.cs.utah.edu/maven/maven-3/3.0.4/binaries/apache-maven-3.0.4-bin.tar.gz
tar -zxvf apache-maven-3.0.4-bin.tar.gz

Now just make sure that either ~/local/src/java/apache-maven-3.0.4/bin is in your path or explicitly call ~/local/src/java/apache-maven-3.0.4/bin/mvn each time. You'll probably want to add something like:

JAVA_HOME=/usr/lib/jvm/java-6-openjdk
PATH="${PATH}":"${HOME}"/local/src/java/apache-maven-3.0.4/bin

To your ~/.bashrc.

source ~/.bashrc

Readying OWLTools

First, we need to download and build OWLTools--it contains the loader code that GO uses for ontology and GAF files, as well as the tools to generate a new Solr schema from AmiGO 2 YAML config files. The code should be self-sufficient and easy to build on a machine with an internet connection.

mkdir -p ~/local/src/svn
cd ~/local/src/svn
svn checkout http://owltools.googlecode.com/svn/trunk/ owltools

To build:

cd ~/local/srv/svn/owltools/OWLTools-Parent/ && mvn clean package

Or, without unit tests (much quicker):

cd ~/local/src/svn/owltools/OWLTools-Parent/ && mvn clean package -DskipTests

The owltools binary should now be built, so you'll probably want to add it to your path by adding the following to your ~/.bashrc:

PATH="${PATH}":"${HOME}"/local/src/svn/owltools/OWLTools-Runner/bin

Then refresh:

source ~/.bashrc

Solr with the GO Solr schema (GOlr)

While we have Jetty installed from the Ubuntu repos, we have our own Solr (3.6, the one that comes with Ubuntu 12.04 is ancient) in the GOlr repo. Let's get that first and look at it; even if we don't use the GOlr repo's supplied schema.xml, some of the information in there can be helpful.

cd ~/local/src/svn
svn co https://geneontology.svn.sourceforge.net/svnroot/geneontology/golr geneontology/golr

While we can install/handle our Jetty/Solr setup with the golr.el script found in this repo, you may find it easier to just look at the script and copy its actions unless you're really into Emacs.

The solr.war for Jetty is at:

~/local/src/svn/geneontology/golr/lib/solr.war

Deploy this either manually or with the the golr.el script found at:

~/local/src/svn/geneontology/golr/tools/golr.el

The golr.el script is a little tricky to make work unless you're really into Emacs, so you may find it easier to just take a look at it and follow along for the parts that you need.

Of course, it's important to remember that the most important end product of this section is to be using a correctly organized schema.xml file in a Solr 3.6 setup. However you accomplish that is fine. For example, the schema.xml file used by GO can be found at:

~/local/src/svn/geneontology/golr/solr/conf/schema.xml

Alternatively, you can generate a custom one by applying an owltools command to a list of YAML config files (as they can be found in the AmiGO 2 repository). As an example, if you haven'y already done so, get the AmiGO 2 code:

mkdir -p ~/local/src/svn
cd ~/local/src/svn
svn co https://geneontology.svn.sourceforge.net/svnroot/geneontology/AmiGO/trunk geneontology/AmiGO/trunk

Then the Solr schema.xml generation would then look like:

owltools --solr-config ~/local/src/git/amigo/metadata/ont-config.yaml ~/local/src/git/amigo/metadata/bio-config.yaml ~/local/src/git/amigo/metadata/ann-config.yaml ~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml --solr-schema-dump

Unfortunately, at this time, this command generates a large amount of unecessary output--everything before the "<?xml version="1.0" ?>" can be thrown away.

Also, the solrconfig.xml file in ~/local/src/svn/geneontology/golr/solr/conf/ might be also be useful in your setup.

Loading the data

As an example, we will load four ontologies useful to GO right now and a single GAF file for annotations onto the localhost Solr instance.

OWLTOOLS_MEMORY=32G owltools http://purl.obolibrary.org/obo/go.owl http://purl.obolibrary.org/obo/ncbitaxon/subsets/taxslim.owl http://purl.obolibrary.org/obo/cl.owl http://purl.obolibrary.org/obo/eco.owl --merge-support-ontologies --reasoner elk --solr-url http://localhost:8080/solr/ --solr-purge --solr-config OWLTOOLS/local/src/svn/geneontology/AmiGO/trunk/metadata/ont-config.yaml --solr-load-ontology --solr-load-panther ~/tmp/PANTHER7.2_HMM_classifications ~/tmp/tree --solr-load-gafs http://www.geneontology.org/gene-associations/gene_association.GeneDB_Lmajor.gz

More memory is always welcome, but less is probably sufficient. The panther section

--solr-load-panther ~/tmp/PANTHER7.2_HMM_classifications ~/tmp/tree

is optional and experimental--it can be left out entirely.

Collaborations

In order to make a truly useful system for the community at large, the Gene Ontology Consortium is working directly with other groups on GOlr tools, schema, and library development.

Virtual Fly Brain (VFB)

We're working with VFB on schema and ontology tools development to help enable rich ontology interaction and search at speed. This will also help push the envelope on the types of use cases that we might see.