Planteome.org - User contributions [en]

AmiGO2 install

2016-11-02T18:46:25Z

Elserj: /* SOLR */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/planteome/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started). Pick either the systemd or init.d version, depending on which init system is being used:

systemd version:
<pre>
[elserj@floret extensions]$ cat /etc/systemd/system/solr.service
[Unit]
Description=Apache Solr
After=syslog.target network.target remote-fs.target nss-lookup.target

[Service]
Type=simple
WorkingDirectory=/data/www/planteome/SOLR/example
ExecStart=/usr/bin/java -jar /data/www/planteome/SOLR/example/start.jar
Restart=on-failure

[Install]
WantedBy=multi-user.target
</pre>

init.d version:
Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
CGI::Application::Plugin::Session
CGI::Application::Plugin::TT
CGI::Application::Plugin::Redirect
DBI
Data::FormValidator
Graph::Directed
XML::Parser
XML::XPath
GraphViz
DBD::SQLite
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

'''This page will be updated as I progress.'''

AmiGO2 install

2016-11-02T18:45:47Z

Elserj: /* SOLR */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/planteome/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

systemd version:
<pre>
[elserj@floret extensions]$ cat /etc/systemd/system/solr.service
[Unit]
Description=Apache Solr
After=syslog.target network.target remote-fs.target nss-lookup.target

[Service]
Type=simple
WorkingDirectory=/data/www/planteome/SOLR/example
ExecStart=/usr/bin/java -jar /data/www/planteome/SOLR/example/start.jar
Restart=on-failure

[Install]
WantedBy=multi-user.target
</pre>

init.d version:
Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
CGI::Application::Plugin::Session
CGI::Application::Plugin::TT
CGI::Application::Plugin::Redirect
DBI
Data::FormValidator
Graph::Directed
XML::Parser
XML::XPath
GraphViz
DBD::SQLite
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

'''This page will be updated as I progress.'''

AmiGO2 install

2016-11-02T18:43:55Z

Elserj: /* SOLR */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/planteome/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

====systemd version====
<pre>
[elserj@floret extensions]$ cat /etc/systemd/system/solr.service
[Unit]
Description=Apache Solr
After=syslog.target network.target remote-fs.target nss-lookup.target

[Service]
Type=simple
WorkingDirectory=/data/www/planteome/SOLR/example
ExecStart=/usr/bin/java -jar /data/www/planteome/SOLR/example/start.jar
Restart=on-failure

[Install]
WantedBy=multi-user.target
</pre>

====init.d version====
Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
CGI::Application::Plugin::Session
CGI::Application::Plugin::TT
CGI::Application::Plugin::Redirect
DBI
Data::FormValidator
Graph::Directed
XML::Parser
XML::XPath
GraphViz
DBD::SQLite
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

'''This page will be updated as I progress.'''

AmiGO2 install

2016-11-02T18:18:51Z

Elserj: /* SOLR */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/planteome/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
CGI::Application::Plugin::Session
CGI::Application::Plugin::TT
CGI::Application::Plugin::Redirect
DBI
Data::FormValidator
Graph::Directed
XML::Parser
XML::XPath
GraphViz
DBD::SQLite
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

'''This page will be updated as I progress.'''

MediaWiki:Spam-whitelist

2016-04-07T15:52:09Z

Elserj: Created page with " # <pre> # External URLs matching this list will *not* be blocked even if they would # have been blocked by blacklist entries. # # Syn..."

# <pre>
# External URLs matching this list will *not* be blocked even if they would
# have been blocked by blacklist entries.
#
# Syntax is as follows:
# * Everything from a "#" character to the end of the line is a comment
# * Every non-blank line is a regex fragment which will only match hosts inside URLs
tinyurl\.com

#</pre>

AmiGO2 install

2016-03-01T21:07:13Z

Elserj: /* Run amigo2 installer */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
CGI::Application::Plugin::Session
CGI::Application::Plugin::TT
CGI::Application::Plugin::Redirect
DBI
Data::FormValidator
Graph::Directed
XML::Parser
XML::XPath
GraphViz
DBD::SQLite
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

'''This page will be updated as I progress.'''

Mar 1st, 2016 Ontology Working Group Meeting

2016-02-29T22:56:02Z

Elserj: /* 3. Update on AmiGO APIs- Justin Elser */

==Planteome Ontology WG Zoom Meeting==
* Date: Tuesday Mar. 1st, 2016
* Time: 8:15am PST (GMT-8)
* Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/762470789

* Links to recordings:
* Attendees:

==Agenda:==
=== 1. Recent updates on the TO ===
* revisions to equivalence axioms- ''occurs_in'' and ''composition''
* Stem and culm
* anther morphology traits, incl. anther number
* biochemical branch

=== 2. Changes and updates in the CO files ===
* rice
* cassava
* lentil

* newly mapped and added- wheat--- TBA

=== 3. Update on AmiGO APIs- Justin Elser ===
* API code changes have been merged into our version of AmiGO (dev.planteome.org)
* Does not work on browser.planteome.org as it will require a reload of all data to work because of a schema change to SOLR
* Small issue with main readme page not showing up, but the API itself is working
** ie. http://dev.planteome.org/api doesn't work
** http://dev.planteome.org/api/entity/term/GO:0022008 works and returns JSON

* Still testing out speed and working on readme page not working

=== 4. Visit to IRRI===
* Leo, Marie-Angelique and Austin will visit IRRI Monday March 7th to Friday March 11th
* Goals: TD revision and data annotation-
** MAL, and Leo will be working on trait dictionary
** AM: annotate 140K+ germplasm entries with PD and TO mapping data

Discussion from email:
* EA- the need for an annotation tool: "We discussed the visit of Marie, Léo and Austin and the agenda we prepared. I indicated Mau that the team would like to see how IRRI data annotations could go on Planteome. Mau asked where Planteome stands with the annotations tools because this what IRRI is waiting for long. Would you have any points you want the team to share with IRRI on that aspect?"
* MAL/LV: "We need a simple tool that scientists will be able to use to easily annotate their data. Adhoc scripts are short term and one-shot solutions that will serve Planteome but not necessarily serve IRRI because: The GAF2 format that amiGO2 requires is not known by the breeding community and the annotated data will be published on Planteome and not in the IRRI information systems. We should take the opportunity of being at IRRI to provide some guidance on how to include the ontologies in their data model. Annotating the data at the source is beneficial for everyone. IRRI information systems will have interoperable and discoverable data. And Planteome can easily add future annotations from the IRRI systems."

== 5. [http://www.phenotypercn.org/?page_id=2750 Phenotype RCN meeting February 26-28, 2016] ==
* PJ attended

== 6. Status of second year funding==
* Bioversity is getting impatient, PJ will follow up with NSF and find out

= Upcoming Meetings and Workshops=
==[https://www.isb-sib.ch/events/biocuration2016/home Biocuration 2016, April 10th-14th,2016; Geneva, Switzerland]==
* MAL is going
** [https://www.isb-sib.ch/events/biocuration2016/key-dates key dates]
** Abstract submitted: https://easychair.org/conferences/submission.cgi?a=10690939;submission=2641703

==[http://blog.garnetcommunity.org.uk/garnetegenis-workshop-integrating-large-data-plant-science-big-data-discovery/ GARNet/Egenis Workshop: Integrating Large Data into Plant Science], April 21st-22nd 2016, Dartington Hall, Totnes, Devon==
* Elizabeth and George are going, EA will present Planteome as part of her talk

== Meeting in Montpellier, May 2016- website??==

==[http://www.bio-ontologies.org.uk/call-for-participation BioOntologies SIG] of the [http://www.iscb.org/ismb2016 Intelligent Systems for Molecular Biology (ISMB)]; July 8-12, 2016, Orlando, Florida ==
* Dates: July 8th and 9th, with July 9th being the “Phenotype Day”, focused on the systematic description of phenotypes.
** Short papers, up to 4 pages (will be published in JBMS)
** Poster abstracts, up to 1 page
** Flash updates, up to 1 page

== [http://icbo.cgrb.oregonstate.edu/ 7th International Conference on Biological Ontology and BioCreative 2016] Aug 1st to 4th, Corvallis, OR==
* Link to program: [http://icbo.cgrb.oregonstate.edu/node/20 ICBO + BioCreative Program]
* Link to Easy Chair site: https://easychair.org/conferences/conference_info.cgi?a=10776589

AmiGO2 install

2016-02-18T22:32:18Z

Elserj: /* Run amigo2 installer */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
CGI::Application::Plugin::Session
CGI::Application::Plugin::TT
CGI::Application::Plugin::Redirect
DBI
Data::FormValidator
Graph::Directed
XML::Parser
XML::XPath
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

'''This page will be updated as I progress.'''

AmiGO2 install

2016-02-17T01:17:00Z

Elserj: /* Notes from older install that may still be relevant */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

'''This page will be updated as I progress.'''

AmiGO2 install

2016-02-17T01:16:32Z

Elserj: /* Run amigo2 installer */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
CGI::Application::Dispatch
CGI::Application::Plugin::Forward
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install that may still be relevant==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Again, earlier install had a missing perl module. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>
<pre>CGI::Application::Dispatch</pre>
'''This page will be updated as I progress.'''

AmiGO2 install

2016-02-17T01:07:20Z

Elserj: /* Run amigo2 installer */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML
Template
Date::Parse
Clone
URI::Escape
JSON::XS
Data::UUID
File::Type
FreezeThaw
WWW::Mechanize
LWP::Protocol::https
</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install that may still be relevant==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Again, earlier install had a missing perl module. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>
<pre>CGI::Application::Dispatch</pre>
'''This page will be updated as I progress.'''

Planteome API discussion

2016-01-29T19:44:26Z

Elserj:

Jan 29, 2016 discussion

* JE, JP, SC, CM, HD

* API needed for bisque integration

* SC - extend out perl API?

* JP - showed old PO web service, require autocomplete

* SC - has to be javascript

* SC - will create ticket in github where we can gather further requirements

Planteome API discussion

2016-01-29T19:42:35Z

Elserj: Created page with "Jan 29, 2016 discussion JE, JP, SC, CM, HD API needed for bisque integration SC - extend out perl API? JP - showed old PO web service, require autocomplete SC - has to be..."

Jan 29, 2016 discussion

JE, JP, SC, CM, HD

API needed for bisque integration

SC - extend out perl API?

JP - showed old PO web service, require autocomplete

SC - has to be javascript

SC - will create ticket in github where we can gather further requirements

AmiGO2 install

2015-12-23T01:57:14Z

Elserj: /* Run amigo2 installer */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

There may be some missing perl packages here. I had to install <pre>Config::YAML</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install that may still be relevant==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Again, earlier install had a missing perl module. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>
<pre>CGI::Application::Dispatch</pre>
'''This page will be updated as I progress.'''

AmiGO2 install

2015-12-23T01:54:45Z

Elserj: /* AmiGO2 install */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Next is to install nodejs (if it isn't already)

On CentOS 6:
<pre>sudo su -
curl --silent --location https://rpm.nodesource.com/setup | bash -
yum install nodejs</pre>
Now to run <pre>npm install</pre> to install necessary nodejs modules.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install that may still be relevant==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Again, earlier install had a missing perl module. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>
<pre>CGI::Application::Dispatch</pre>
'''This page will be updated as I progress.'''

AmiGO2 install

2015-12-23T00:04:24Z

Elserj: /* Configure Apache2 */

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Now to run <pre>npm install</pre>

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>wget ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install that may still be relevant==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Again, earlier install had a missing perl module. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>
<pre>CGI::Application::Dispatch</pre>
'''This page will be updated as I progress.'''

AmiGO2 install

2015-12-22T23:43:40Z

Elserj:

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:
<pre>
[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose
</pre>

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Now to run <pre>npm install</pre>

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install that may still be relevant==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Again, earlier install had a missing perl module. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>
<pre>CGI::Application::Dispatch</pre>
'''This page will be updated as I progress.'''

AmiGO2 install

2015-11-12T22:57:49Z

Elserj:

== GOLR install: ==
Install the 3.6 version of SOLR

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:

[elserj@palea amigo]$ diff /etc/init.d/solr /etc/init.d/solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar /data/www/planteome_dev/SOLR/example/start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep -v planteome_dev2 | grep planteome_dev | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose

At this point, SOLR is now running. Next is to load data to it.

==AmiGO2 install==
Copy the example amigo.yaml file and make the following changes:
<pre>
[elserj@palea conf]$ diff amigo.yaml examples/amigo.yaml.localhost-planteome
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo/go.cgi
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev2/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://test.planteome.org
---
> value: http://localhost:9999
32a33,37
> - model_annotation
> - noctua_model_meta
> - family
> - general
> - bbop_term_ac
40c45
< value: http://galaxy.planteome.org/
---
> value: http://galaxy.berkeleybop.org/
42c47
< comment: 'The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.'
---
> comment: The public URL of the GOlr server (including slash); this is the one called by AmiGO resource, JS, etc.
44c49
< value: http://test.planteome.org/solr/
---
> value: http://dev.planteome.org/solr/
48c53
< value: http://noctua.planteome.org/
---
> value: http://noctua.berkeleybop.org/
52c57
< value: /data/www/planteome_dev2/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
56c61
< value: test.planteome.org
---
> value: localhost
60c65
< value: /data/www/planteome_dev2/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
64c69
< value: http://test.planteome.org/static
---
> value: http://localhost:9999/static
68c73
< value: 'all|[PGTE]O:[0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
76c81
< value: 1.0
---
> value: 2.3.2
78c83
< comment: 'Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.'
---
> comment: Please enter the full path to readable/writable directory that will be used for things like temporary files, logs (if enabled), and the golr_timestamp.log file.
89,91c94,98
< - file:///data/www/planteome_dev/amigo/associations/eo-associations/eo_diversity_arabidopsis.assoc
< - file:///data/www/planteome_dev/amigo/associations/po-associations/po_anatomy_gene_arabidopsis_tair.assoc
< - file:///data/www/planteome_dev/amigo/associations/to-associations/to_diversity_arabidopsis.assoc
---
> - http://www.geneontology.org/gene-associations/gene_association.mgi.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_ref_human.gz
> - http://www.geneontology.org/gene-associations/gene_association.goa_uniprot_noiea.gz
> - http://www.geneontology.org/gene-associations/gene_association.reactome.gz
96,99c103,110
< - /data/www/planteome_dev/amigo/metadata/ont-config.yaml
< - /data/www/planteome_dev/amigo/metadata/bio-config.yaml
< - /data/www/planteome_dev/amigo/metadata/ann-config.yaml
< - /data/www/planteome_dev/amigo/metadata/general-config.yaml
---
> - '~/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/general-config.yaml'
> - '~/local/src/git/amigo/metadata/model-ann-config.yaml'
> - '~/local/src/git/amigo/metadata/noctua-model-meta-config.yaml'
> - '~/local/src/git/amigo/metadata/protein-family-config.yaml'
> - '~/local/src/git/amigo/metadata/ann_ev_agg-config.yaml'
103c114
< value: /data/www/planteome_dev2/amigo/metadata/ont-config.yaml
---
> value: '~/local/src/git/amigo/metadata/ont-config.yaml'
107c118
< value: /data/www/planteome_dev2/noctua-models/models/
---
> value: '~/local/src/git/noctua-models/models/'
112c123
< - file:///data/www/planteome_dev2/amigo/ontology_files/planteome.owl
---
> - http://purl.obolibrary.org/obo/go/extensions/go-plus.owl
120c131
< value: 20G
---
> value: 3G
</pre>

Now to run <pre>npm install</pre>

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The log files need to be created or else Apache will not start:
<pre>mkdir log
touch log/access.log
touch log/error.log
sudo chown root: log/*.log
</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

===Run amigo2 installer===
<pre>./node_modules/.bin/gulp install</pre>

===Load ontologies===
<pre>./node_modules/.bin/gulp load-ontology</pre>

===Load associations===
<pre>./node_modules/.bin/gulp load-gafs</pre>

At this point Amigo2 appears to be working.

==Notes from older install that may still be relevant==
At one point from doing an older install, it needed a missing yui-compressor, so need to get that installed. (May no longer be relevant)
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Again, earlier install had a missing perl module. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>
<pre>CGI::Application::Dispatch</pre>
'''This page will be updated as I progress.'''

Oct 27th, 2015 Ontology Working Group Meeting

2015-10-28T19:35:40Z

Elserj: /* Questions about Customization of the Planteome AmiGO 2.x version: */

=Planteome Ontology WG Zoom Meeting=
* Time: Oct 27th, 2015 8:15 AM (GMT-7:00) Pacific Time (US and Canada)
* Connection info: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/672187671

* [[File:Ontology WG 10-27-15 video.mp4|thumb|Ontology WG 10-27-15 video]]
* [[File:Ontology WG 10-27-15 audio.m4a|thumb|Ontology WG 10-27-15 audio]]

==Planning for the Fall Workshop in Corvallis==
Discussion of the Agenda: see link
[https://docs.google.com/spreadsheets/d/1hwltFYdp3bGK_3VGEr9Ep5fOeAj1VC2ZThxrBGONrXQ/edit?usp=sharing Corvallis Ontology Workshop Agenda- Nov. 2015- DRAFT]

==Ontology term discussion==
* see https://github.com/Planteome/plant-ontology/issues/607

==Progress on Updating AmiGO 2 Browser==
* Follow up call 10-27-15 with JE, LC, SC, CM

* Link to recordings:
** [[File:AmiGO 2.0 10-27-2015 audio.m4a|thumb|AmiGO 2.0 10-27-2015 audio]]
** [[File:AmiGO 2.0 10-27-2015 video p1.mp4|thumb|AmiGO 2.0 10-27-2015 video p1]]
** [[File:AmiGO 2.0 10-27-2015 video p2.mp4|thumb|AmiGO 2.0 10-27-2015 video p2]]

===Questions about Customization of the Planteome AmiGO 2.x version:===
From the email discussion:
* '''Customizing templates:''' Is there a way to just specify a new template path? I can modify the files in the current templates folder, but this seems like the wrong way to do it.
** ''SC:Yes there is, although it has not been specified as a config variable (we can change that)--we kept this usecase in mind during the last major refactor. That said, it might be doable to simply have a fork that changes the template pathing variable--that way you could stay current and still make arbitrary changes.''
** Seth is making the change in upstream AmiGO on git. As long as our fork is merged and we moved to match current master, this will happen soon.

* '''xrefs: How can I add new xrefs so that the links in the "Mappings"tabs work?'''- In 1.5, I would modify Namemunger.pm, in 1.8 I would modify go-db-perl/t/data/GO.xrf_abbs then run a modified make_dblinks.pl that didn't pull the GO.xrf_abbs file from CVS new each time, but this always seemed like a terrible hack on my part. Even so, I don't see a comparable method in AmiGO2. I'm sure there is a better way to do it.
** ''SC: We're all about yaml files now https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml Depending on the exact use, the YAML files are only part of it: we also have all sorts of customizable low-level overrides for various display handlers, as well as easy overrides in the JS linker "class". Again, it's easy enough to isolate that particular YAML pick-up as a variable and generalize it all.''
** Discussion also pointed out that we can modify this in git and have it pushed to upstream. All xrefs would then be globally available.

* '''What adds the text to "Last file loaded on"?''' On mine, it just has "???". I thought I found this once, but can't find it again, and thought this would be part of the golr/Makefile.
** SC: This is generated by a specially structured (simple TSV) file generated by the loader; if found, as specified by a runtime variable, it will display the date, etc

* '''Filters not being saved on clicking back'''- we already have issue tracker open: [https://github.com/geneontology/amigo/issues/50 #50]- Is this something that can be fixed easily downstream??
** ''SC: No, it's something that I'm personally not a huge fan of behavior-wise. We have a fairly good bookmarking mechanism now that could help out with that, but some nice re-draw code would have to be added so it wasn't excessively "jerky".''

* '''Being able to pin multiple filters,''' i.e. being able to select both "plant_anatomy" and "plant_trait_ontology" from the list of "Ontology sources" at the same time, or being able to select multiple species in the annotation search. I suppose this works by selecting the "-" rather than the "+" and choosing all the ones we don't want, but it seems a bit more intuitive to choose the ones we do want rather than those we don't. Plus we have something like 50 species, and probably will add more moving forward.
** ''SC: In addition to what Chris mentioned, there are a couple of options that could be explored at the manager API level that might not be too disruptive, but would require a little work, see: [https://github.com/berkeleybop/bbop-js/issues/5 #5]. While icky, this is something that can also be specified at the Solr level, but I wouldn't. ''

Notes from Meeting:
* Question and discussion about the best way to keep in sync with the revised version of AmiGO2- recommend making a new fork with the new version (2.3x) and adding in the customizations
* Timeline for rolling out??
* Using master vs a branch?
* Goal is to move main Planteome page to the AmiGO 2.0
* Do we need a separate SolR instance? Need to go through Sys admin- Chris Sullivan

From cjm : http://dev.planteome.org/amigo/search/ontology

From cjm : Japanese
* Japanese fonts were fixed in master.

From sjcarbon : https://github.com/geneontology/go-site

From sjcarbon : https://github.com/geneontology/amigo
* Planteome fork was created https://github.com/Planteome/amigo

==Revisions to the Trait Ontology==

==Other upcoming meetings and workshops==
** PAG 2016
** ICBO 2016

Oct 20th, 2015 Ontology Working Group Meeting

2015-10-20T15:39:07Z

Elserj: /* Transition to AmiGO2- Status report */

=Planteome Ontology WG Zoom Meeting=
* Time: Oct 20, 2015 8:15 AM (GMT-7:00) Pacific Time (US and Canada)

Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/592326941

Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/592326941

Who: LC, AM, CM, PJ, JE, EA, MAL

Regrets:

* Link to recording- Video: tba
* Link to recording- Audio: tba

==Planteome workshop Nov 9-13th, ==
* Location: Oregon State University, Corvallis, 2nd week of Nov
* For more details- please see the notes are on the wiki- [[Planteome_Curator_workshop_Fall_2015]]

==Plant Ontology Release #21 ==
- Many changes and updates to the PO
* Transition to GitHub complete, and working well- required many updated Xrefs and links in the various browsers, ontology files and pages.
* PO Live Browser updated for the transition to GitHub with links to the new Issue Tracker and association repository on the SVN-
*
* For more information: [http://wiki.plantontology.org/index.php/Release_21 Plant_Ontology_Release_#21]

* New association data developed from the [http://wiki.plantontology.org/index.php/Plant_Pheontype_Pilot_Project_2015] paper published in Feb 2015: http://www.plantmethods.com/content/11/1/10/abstract
** Six plant species: Rice, Maize, Arabidopsis, soybean, Medicago, tomato ~ 4,193 new direct associations

== Discussion about Plant Trait Ontology==
See notes on: [[Sept_15th,_2015-_Ontology_Working_Group_Meeting#3._Plant_Trait_Ontology]]

== Transition to AmiGO2- Status report ==
* Link to [http://dev.planteome.org/amigo/search/ontology Dev.Planteome site]

* Link to Issue Tracker on GitHub: [https://github.com/Planteome/planteome-ontology-browsers/issues]

* Working on getting AmiGO instances up for live site (and second dev site for Data Visualization group). Waiting for Chris Sullivan to okay changes to server.

==PAG 2016: Systems Biology and Ontologies Workshop==
* Saturday Jan 9th, 8 am
* Link to PAG webpage: [https://pag.confex.com/pag/xxiv/webprogram/Session3177.html Systems Biology and Ontologies]

==Planteome Curator Workshop at PAG==

==ICBO Conference Planning==
Conference webpage: [http://icbo.cgrb.oregonstate.edu/ ICBO 2016]

==Next Ontology Meeting Tuesday Oct 27th==

MediaWiki:Public read whitelist

2015-09-30T20:30:51Z

Elserj: Created page with "Planteome_Curator_workshop_Fall_2015"

Planteome_Curator_workshop_Fall_2015

AmiGO2 install

2015-09-17T22:02:41Z

Elserj: /* GOLR install: */

== GOLR install: ==
There are a few prerequisites to getting GOLR installed. They appear to be Maven and OwlTools. To install maven, I followed the instructions from here: http://blog.gluster.org/2013/08/yum-install-maven-yes-you-can/, seemed to work without error.

===OWLTools===
Then, to install OWLTools, I did the following:
<pre>
cd /lemma/justin
svn co http://owltools.googlecode.com/svn/trunk/ owltools
</pre>
This creates the owltools directory in my space on lemma.

To compile OWLTools, run:
<pre>
cd OWLTools-Parent
mvn clean package
</pre>
This will take about half an hour.

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /data/www/planteome_dev/SOLR/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:

<pre>elserj@palea init.d]$ diff solr solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep start.jar | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose</pre>

At this point, SOLR is now running. Next is to load data to it.

==Load data into GOLR instance==
First we need to pull down the latest AmiGO code from git:
<pre>cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

In the <i>metadata</i> folder are the yaml files that tell owltools how to populate the fields in GOLR

Edit the golr/Makefile to fit our server:
<pre>[elserj@palea golr]$ diff Makefile Makefile.org
18c18
< MAVEN_EXE ?= /usr/bin/mvn
---
> MAVEN_EXE ?= ~/local/src/java/apache-maven-3.0.4/bin/mvn
21c21
< SOLR_URL ?= http://dev.planteome.org:8983/solr
---
> SOLR_URL ?= http://localhost:8080/solr/
24,27c24,27
< OWLTOOLS_ROOT ?= /nfs0/BPP/Jaiswal_Lab/justin/owltools/
< BBOP_JS_ROOT ?= /data/www/planteome_dev/amigo/external/
< #PANTHER_FILES_DIR ?= ~/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/
< #SOLR_DATA_ROOT ?= /srv/solr
---
> OWLTOOLS_ROOT ?= ~/local/src/git/owltools/
> BBOP_JS_ROOT ?= ~/local/src/git/bbop-js/
> PANTHER_FILES_DIR ?= ~/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/
> SOLR_DATA_ROOT ?= /srv/solr</pre>

===load-ontology===
Try to run the load-ontology part of the Makefile:
<pre>make load-ontology</pre>

This will take some time as it appears to be updating the owltools and then loading the ontologies

At this point, I get an error when trying to load the ontologies. Working with Seth to figure it out.

Errors were mostly caused by memory issues. Had to comment out the ncbitaxon.owl ontology from the list of ones ran. Upped the memory to 20GB on palea. May eventually have to look at running the load on one of the cluster nodes as they have much more RAM. Would have to figure out how to open up the SOLR port to the internal network though.

Now to get annotation test data into GOLR
<pre>make load-test-gaf</pre>
This took a few minutes to run, not long.

At this point, data for an initial test is loaded into SOLR, next is to get AmiGO2 up and running off that instance.

==AmiGO2 install==
Since we already have pulled the amigo code from git, we have to work on configuring it:

<pre>cd amigo/conf
cp .initial_values.yaml amigo.yaml
</pre>

Change the amigo.yaml file as follows:
<pre>[elserj@palea conf]$ diff amigo.yaml .initial_values.yaml
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://dev.planteome.org
---
> value: http://localhost:9999
33c33
< value: http://dev.planteome.org/solr/
---
> value: http://localhost:8080/solr/
37c37
< value: /data/www/planteome_dev/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
41c41
< value: planteome-dev
---
> value: localhost
45c45
< value: /data/www/planteome_dev/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
49c49
< value: http://dev.planteome.org/static
---
> value: http://localhost:9999/static
53c53
< value: 'all|[GPTE]O:[u0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
65c65
< value: /data/www/planteome_dev/amigo/golr_timestamp.log
---
> value: /home/sjcarbon/local/src/git/amigo/golr_timestamp.log
69c69
< value: /data/planteome_dev/amigo/external/bbop.js
---
> value: /home/sjcarbon/local/src/git/amigo/external/bbop.js
73c73
< value: /data/www/planteome_dev/amigo/metadata
---
> value: /home/sjcarbon/local/src/git/amigo/metadata
</pre>

Now to run <pre>make install</pre>

This gives an error about a missing yui-compressor, so need to get that installed.
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Next problem is that rhino gives an error message about "invalid option modules". Still communicating with Seth on solution. Will update when solution found.

Solution was to comment out the test and docs part of the install target in the Makefile. Rhino was apparently only used for unit testing, which we don't really need to do.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

doing the <pre>make install</pre> now works without error.

However, the server doesn't work when navigated to. It looks like a perl module is missing. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>

Error is now about "Type of arg 1 to keys must be hash" Will work on this error.

This error apparently is the result of the older version of perl that we have installed. Seth fixed this in git, so I did a git pull and got past it.

However, another perl module needed to be installed via cpan:
<pre>CGI::Application::Dispatch</pre>

At this point Amigo2 appears to be working.

'''This page will be updated as I progress.'''

Data storage and AmiGO 2 Working Group Meetings

2015-09-15T20:54:35Z

Elserj:

=Data storage and AmiGO 2 call 1-30-15=
* Who: PJ, CM, Seth, EZ, LC, JP, JE
* Discussion of the planned transition to the AmiGO 2.0 platform
* JE is working on installing SolR database - View details and progress reports here: [[AmiGO2_install]]

= Data Storage and AmiGO2 call 2-18-15=
* Who: JE, JP, EZ
* Link to video recording: [[Media:Data_Storage_2-18-15.mp4]]
* Link to audio recording: [[File:Data Storage Meeting audio only 2-18-15.m4a|thumbnail|Data_Storage_Meeting_audio_only_2-18-15.m4a]]

* Further discussion of AmiGO2 progress and overview of AmiGO2 interface

=Planteome Interface meeting 3-2-15=
Who: EZ, LC, JE, PJ ...??
* Link to video recording: [[File:Planteome Interface mtg video 3-2-15.mp4|thumbnail|Planteome_Interface_mtg_video_3-2-15.mp4]]
* Link to audio recording: [[File:Planteome Interface mtg audio 3-2-15.m4a|thumbnail|Planteome Interface mtg audio 3-2-15.m4a]]

* EZ: First thing: focus of the project, speed up queries, data visualization, data organization
* User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
* Amigo 2, could build enhanced interface so users could inspect their data and build queries.
* what functionalities are needed?
* Questions:
**How will the users access the interface?
** How will they use the interface?
==Involvement of other organisms? e.g. viruses, animals, etc==
* Could the tools be expanded to other organisms
* Crops are interacting with the environment, other organisms
== AmiGO2 introduction==
* show filtered image
* Cytoscape Sif file, ontology network
* bring in other ontologies, Rice Xanthomanas example
* ontology formats

=Data storage and AmiGO2 Working Group Meeting 4-16-15=

Who: EZ, BQ, PJ, JP, LC, JE

* Link to video recording: [[File:Data_storage_and_AmiGO2_video_4-16_15.mp4|thumbnail|Data_storage_and_AmiGO2_video_4-16_15.mp4]]
* Link to audio recording: [[File:Data storage and AmiGO2 audio 4-16 15.m4a|thumbnail|Data storage and AmiGO2 audio 4-16 15.m4a]]

* Introductions
* Storing code developed on Planteome project on Github
* posting notes on wiki
* data visualization aspect within AmiGO2- work with JE on
* Data annotation- wikipedia style?
* different levels of access
* To do: Send link to Eugene and Botong- circulate the developer position ad

==Relevant links:==
* https://github.com/geneontology/amigo
* Demo: http://amigo.geneontology.org/
* http://amigo2.berkeleybop.org/ - dev server

=Data storage and AmiGO2 Working Group meeting 5-1-15=
Who: PJ, BQ, EZ, CM, JE
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]
* Link to audio: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]

==Demo of GO enrichment tool==
*At the GO website (www.geneontology.org)
*See how it works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.

*Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
* Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
*Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.
This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.

I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.

BinGO
http://bioinformatics.oxfordjournals.org/content/21/16/3448.full
AgriGO
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/

=Data storage and AmiGO2 Working Group Meeting 5-15-15=
Who: PJ, EZ, BQ, JE, CM

*Continue to show how the enrichment analysis tools work(agriGO).
*Discuss about the language and character problem on the page.
*Agreed to start with design the requirement specification.
*Share the old database scheme with EZ and BQ.
*Show the Annotation database to EZ and BQ (unfinished, need to be continued).

EZ and BQ will start with analyzing the old database scheme and try to study the enrichment analysis algorithms, the first goal of the group is to show the search result through tables. The next step will be visualize it with Graph.

=Data storage and visualization Working Group Meeting 5-27-15=
Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)

==Link to recordings (in 2 parts):==
* Audio P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a|thumbnail|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]
* Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4|thumbnail|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]
* Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a|thumbnail|Data_Visualization_5-27-15_audio.m4a]]
* Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4|thumbnail|Data_Visualization_5-27-15_part_2.mp4]]

==Intro to Planteome for to new students==
* Explanation of ontologies
* Overview of older AmiGO browser
* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology [http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php]
** Used gene set from planteome.cgrb to demonstrate AgriGO usage

=Data storage and visualization Working Group Meeting 6-3-15=
Who: EZ, PJ, LC, JP, Christian and Marquis (REU students)
Location: Kelley 2057 (KEC)

===Link to recordings (in 3 parts):===
* Video P.1: [[File:Data Store meeting p1 6-3-15 video.mp4|thumbnail|Data Store meeting p1 6-3-15 video.mp4]]
* Video P.2: [[File:Data Store meeting p2 6-3-15 video.mp4|thumbnail|Data Store meeting p2 6-3-15 video.mp4]]
* Video P.3: [[File:Data Store Meeting p3 6-3-15 video.mp4|thumbnail|Data Store Meeting p3 6-3-15 video.mp4]]

==Database discussion==
* Discussion of the legacy gene database schema for the Plant Ontology - 36 tables

Example fields in gene table

{| class="wikitable"
|-
! field name !! comment
|-
|gene symbol || ? ||
|-
|gene name || ? ||
|-
|synonyms || one to many ||
|-
| ontology ID ||Ontology term name ||
|-
| || ||
|-
| || ||
|-
| || ||
|-

=Data storage and visualization Working Group Meeting 8-26-15=
Who: EZ, PJ, JE, Jaden, Botong, CM
Location: Kelley 2057 (KEC)

===Link to recording===
* Video: [[File:Data_Visualization_Meeting_8-26-15.mp4|thumbnail|Data_Visualization_Meeting_8-26-15.mp4]]

===Discussion===
Discussion was on the document that Botong wrote outlining the groups role and history in the Planteome project. Discussed design and implementation of the GCT (Gene Curation Tool) they are designing. Chris Mungall joined the call after about 40 minutes and demo'd the Noctua tool that they have been developing.

=Data storage and visualizaion Working Group Meeting 9-15-15=
Who:
Location: Kelley 1114

===Discussion===
Discussion was on what the focus should be for the group. Group should focus on the statistics and data storage for now. Visualization will be worked on later. Rest of discussion was of integration of AmiGO2 and something like AgriGO functionality.

Data storage and AmiGO 2 Working Group Meetings

2015-09-15T19:02:28Z

Elserj:

=Data storage and AmiGO 2 call 1-30-15=
* Who: PJ, CM, Seth, EZ, LC, JP, JE
* Discussion of the planned transition to the AmiGO 2.0 platform
* JE is working on installing SolR database - View details and progress reports here: [[AmiGO2_install]]

= Data Storage and AmiGO2 call 2-18-15=
* Who: JE, JP, EZ
* Link to video recording: [[Media:Data_Storage_2-18-15.mp4]]
* Link to audio recording: [[File:Data Storage Meeting audio only 2-18-15.m4a|thumbnail|Data_Storage_Meeting_audio_only_2-18-15.m4a]]

* Further discussion of AmiGO2 progress and overview of AmiGO2 interface

=Planteome Interface meeting 3-2-15=
Who: EZ, LC, JE, PJ ...??
* Link to video recording: [[File:Planteome Interface mtg video 3-2-15.mp4|thumbnail|Planteome_Interface_mtg_video_3-2-15.mp4]]
* Link to audio recording: [[File:Planteome Interface mtg audio 3-2-15.m4a|thumbnail|Planteome Interface mtg audio 3-2-15.m4a]]

* EZ: First thing: focus of the project, speed up queries, data visualization, data organization
* User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
* Amigo 2, could build enhanced interface so users could inspect their data and build queries.
* what functionalities are needed?
* Questions:
**How will the users access the interface?
** How will they use the interface?
==Involvement of other organisms? e.g. viruses, animals, etc==
* Could the tools be expanded to other organisms
* Crops are interacting with the environment, other organisms
== AmiGO2 introduction==
* show filtered image
* Cytoscape Sif file, ontology network
* bring in other ontologies, Rice Xanthomanas example
* ontology formats

=Data storage and AmiGO2 Working Group Meeting 4-16-15=

Who: EZ, BQ, PJ, JP, LC, JE

* Link to video recording: [[File:Data_storage_and_AmiGO2_video_4-16_15.mp4|thumbnail|Data_storage_and_AmiGO2_video_4-16_15.mp4]]
* Link to audio recording: [[File:Data storage and AmiGO2 audio 4-16 15.m4a|thumbnail|Data storage and AmiGO2 audio 4-16 15.m4a]]

* Introductions
* Storing code developed on Planteome project on Github
* posting notes on wiki
* data visualization aspect within AmiGO2- work with JE on
* Data annotation- wikipedia style?
* different levels of access
* To do: Send link to Eugene and Botong- circulate the developer position ad

==Relevant links:==
* https://github.com/geneontology/amigo
* Demo: http://amigo.geneontology.org/
* http://amigo2.berkeleybop.org/ - dev server

=Data storage and AmiGO2 Working Group meeting 5-1-15=
Who: PJ, BQ, EZ, CM, JE
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]
* Link to audio: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]

==Demo of GO enrichment tool==
*At the GO website (www.geneontology.org)
*See how it works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.

*Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
* Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
*Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.
This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.

I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.

BinGO
http://bioinformatics.oxfordjournals.org/content/21/16/3448.full
AgriGO
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/

=Data storage and AmiGO2 Working Group Meeting 5-15-15=
Who: PJ, EZ, BQ, JE, CM

*Continue to show how the enrichment analysis tools work(agriGO).
*Discuss about the language and character problem on the page.
*Agreed to start with design the requirement specification.
*Share the old database scheme with EZ and BQ.
*Show the Annotation database to EZ and BQ (unfinished, need to be continued).

EZ and BQ will start with analyzing the old database scheme and try to study the enrichment analysis algorithms, the first goal of the group is to show the search result through tables. The next step will be visualize it with Graph.

=Data storage and visualization Working Group Meeting 5-27-15=
Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)

==Link to recordings (in 2 parts):==
* Audio P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a|thumbnail|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]
* Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4|thumbnail|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]
* Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a|thumbnail|Data_Visualization_5-27-15_audio.m4a]]
* Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4|thumbnail|Data_Visualization_5-27-15_part_2.mp4]]

==Intro to Planteome for to new students==
* Explanation of ontologies
* Overview of older AmiGO browser
* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology [http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php]
** Used gene set from planteome.cgrb to demonstrate AgriGO usage

=Data storage and visualization Working Group Meeting 6-3-15=
Who: EZ, PJ, LC, JP, Christian and Marquis (REU students)
Location: Kelley 2057 (KEC)

===Link to recordings (in 3 parts):===
* Video P.1: [[File:Data Store meeting p1 6-3-15 video.mp4|thumbnail|Data Store meeting p1 6-3-15 video.mp4]]
* Video P.2: [[File:Data Store meeting p2 6-3-15 video.mp4|thumbnail|Data Store meeting p2 6-3-15 video.mp4]]
* Video P.3: [[File:Data Store Meeting p3 6-3-15 video.mp4|thumbnail|Data Store Meeting p3 6-3-15 video.mp4]]

==Database discussion==
* Discussion of the legacy gene database schema for the Plant Ontology - 36 tables

Example fields in gene table

{| class="wikitable"
|-
! field name !! comment
|-
|gene symbol || ? ||
|-
|gene name || ? ||
|-
|synonyms || one to many ||
|-
| ontology ID ||Ontology term name ||
|-
| || ||
|-
| || ||
|-
| || ||
|-

=Data storage and visualization Working Group Meeting 8-26-15=
Who: EZ, PJ, JE, Jaden, Botong, CM
Location: Kelley 2057 (KEC)

===Link to recording===
* Video: [[File:Data_Visualization_Meeting_8-26-15.mp4|thumbnail|Data_Visualization_Meeting_8-26-15.mp4]]

===Discussion===
Discussion was on the document that Botong wrote outlining the groups role and history in the Planteome project. Discussed design and implementation of the GCT (Gene Curation Tool) they are designing. Chris Mungall joined the call after about 40 minutes and demo'd the Noctua tool that they have been developing.

=Data storage and visualizaion Working Group Meeting 9-15-15=
Who:
Location: Kelley 1114

===Link to recording===
Not available yet

===Discussion===

Data storage and AmiGO 2 Working Group Meetings

2015-08-27T20:47:25Z

Elserj:

File:Data Visualization Meeting 8-26-15.mp4

2015-08-27T20:42:15Z

Elserj: Video recording of the Zoom conference call of the Data Visualization group meeting on Aug 26, 2015.

Video recording of the Zoom conference call of the Data Visualization group meeting on Aug 26, 2015.

Data storage and AmiGO 2 Working Group Meetings

2015-08-27T20:29:15Z

Elserj:

Svn migration to git

2015-08-22T04:18:59Z

Elserj: /* Filtering the dump */

=Migration of the ontology respository from svn to git=

==Motivation==

After much discussion with Chris Mungall, it was decided to migrate all relevant files from the POC svn repo to a new planteome repository in [github http://github.com].

Not all files are needed to be moved. Most notably, the association files are too large to be hosted on github, so we are looking for a solution for this.

Also, ontology files besides the plant_ontology.obo file were stored in a collaborators_ontology folder. We decided to restructure the repo to make these at the same level

==Dumping the svn repo==

To keep the revision info for the files, we need to dump all of that from svn and then filter it out for the specific files we need to move to git.

On Palea
<pre>cd /data/svnrepos/Poc
svnadmin dump . > /lemma/justin/Poc_svn_migration/Poc_svn_dump
</pre>

This will dump all repo information including revision info and commit messages to a file named Poc_svn_dump. I stored this on lemma as the file is large (>25GB).

===Filtering the dump===
Note: the following was run on one of cluster compute nodes because I didn't want to swamp palea working on it.

I decided to test this out with trait.obo first as a proof of concept. Other files should be similar with changes to the include statement
<pre>cd /lemma/justin/Poc_svn_migration
cat Poc_svn_dump | svndumpfilter include /trunk/ontology/collaborators_ontology/gramene/traits/trait.obo --drop-empty-revs --renumber-revs > trait.obo_filtered_dump
</pre>

The <pre>svndumpfilter</pre> command will go through the dump file and only output revision info for trait.obo, in this case. The full path needs to be in the include argument, otherwise it output an empty repo. The other arguments will reset the revision numbers so that they start at 1 and have no empty revisions.

If the file path needs to be changed, this is the point to do it. Here is a command that I used to change the filename and remove the full path:
<pre>
cat trait.obo_filtered_dump | sed 's/Node-path: trunk\/ontology\/collaborators_ontology\/gramene\/traits\//Node-path: plant-trait-ontology.obo/' > trait.obo_filtered_path_fixed_dump
</pre>

For repos that have had files moved with history before, the above did not work when trying to import into repo in the next step. I used the following for a different repo to get it to work:
<pre>cat associations_dump | sed 's/Node-path: trunk\/associations/Node-path: po-associations/' | sed 's/Node-copyfrom-path: trunk\/associations/Node-copyfrom-path: po-associations/' > associations_filtered_path_dump
</pre>

==Create a new svn repo to hold the filtered data==
<pre>cd /data/svnrepos
sudo svnadmin create /data/svnrepos/svn2git
sudo chown -R apache: svn2git</pre>

==Copy the filtered dump to the new repo==
Then back on palea (svn server):
<pre>cd /data/svnrepos
sudo svnadmin load ./svn2git < /lemma/justin/Poc_svn_migration/trait.obo_filtered_path_fixed_dump
</pre>

At this point, we should have a fresh clean svn repo with only the filtered files in it with all revision info.

==Copy the svn repo to github==
===Method if repo in github hasn't been created yet (simpler)===
Go to https://import.github.com/new and follow the steps there. This will use the SVN repo created above.

===Method if github repo already has files in it===
I couldn't figure out how to do this direct from the svn, but I figured out how to do it by using an intermediate temporary github repo.

Create a new temporary github repo from the svn using the "simpler" import method described above.

In this example, I created a temporary github repo https://github.com/elser/dbxref that contained just the PO_DBXref.txt file along with its history. I wanted to move it to the Planteome/common-files-for-ref-ontologies repo under Planteome.
<pre>mkdir git_temp
cd git_temp/
git clone https://github.com/elserj/dbxref.git dbxref
cd dbxref/
git remote rm origin
git filter-branch --subdirectory-filter dbxref -- --all
git commit
cd ../
git clone https://github.com/Planteome/common-files-for-ref-ontologies.git common-files-for-ref-ontologies
cd common-files-for-ref-ontologies/
git remote add origin-dbxref ../dbxref
git pull origin-dbxref master
git remote rm origin-dbxref
git push</pre>

Note that not every line is required, noticeably the "git filter-branch", but they may be needed if the repo has multiple folders or other structure that this example didn't have.

Svn migration to git

2015-08-22T00:37:32Z

Elserj: /* Filtering the dump */

=Migration of the ontology respository from svn to git=

==Motivation==

After much discussion with Chris Mungall, it was decided to migrate all relevant files from the POC svn repo to a new planteome repository in [github http://github.com].

Not all files are needed to be moved. Most notably, the association files are too large to be hosted on github, so we are looking for a solution for this.

Also, ontology files besides the plant_ontology.obo file were stored in a collaborators_ontology folder. We decided to restructure the repo to make these at the same level

==Dumping the svn repo==

To keep the revision info for the files, we need to dump all of that from svn and then filter it out for the specific files we need to move to git.

On Palea
<pre>cd /data/svnrepos/Poc
svnadmin dump . > /lemma/justin/Poc_svn_migration/Poc_svn_dump
</pre>

This will dump all repo information including revision info and commit messages to a file named Poc_svn_dump. I stored this on lemma as the file is large (>25GB).

===Filtering the dump===
Note: the following was run on one of cluster compute nodes because I didn't want to swamp palea working on it.

I decided to test this out with trait.obo first as a proof of concept. Other files should be similar with changes to the include statement
<pre>cd /lemma/justin/Poc_svn_migration
cat Poc_svn_dump | svndumpfilter include /trunk/ontology/collaborators_ontology/gramene/traits/trait.obo --drop-empty-revs --renumber-revs > trait.obo_filtered_dump
</pre>

The <pre>svndumpfilter</pre> command will go through the dump file and only output revision info for trait.obo, in this case. The full path needs to be in the include argument, otherwise it output an empty repo. The other arguments will reset the revision numbers so that they start at 1 and have no empty revisions.

If the file path needs to be changed, this is the point to do it. Here is a command that I used to change the filename and remove the full path:
<pre>
cat trait.obo_filtered_dump | sed 's/Node-path: trunk\/ontology\/collaborators_ontology\/gramene\/traits\//Node-path: plant-trait-ontology.obo/' > trait.obo_filtered_path_fixed_dump
</pre>

==Create a new svn repo to hold the filtered data==
<pre>cd /data/svnrepos
sudo svnadmin create /data/svnrepos/svn2git
sudo chown -R apache: svn2git</pre>

==Copy the filtered dump to the new repo==
Then back on palea (svn server):
<pre>cd /data/svnrepos
sudo svnadmin load ./svn2git < /lemma/justin/Poc_svn_migration/trait.obo_filtered_path_fixed_dump
</pre>

At this point, we should have a fresh clean svn repo with only the filtered files in it with all revision info.

==Copy the svn repo to github==
===Method if repo in github hasn't been created yet (simpler)===
Go to https://import.github.com/new and follow the steps there. This will use the SVN repo created above.

===Method if github repo already has files in it===
I couldn't figure out how to do this direct from the svn, but I figured out how to do it by using an intermediate temporary github repo.

Create a new temporary github repo from the svn using the "simpler" import method described above.

In this example, I created a temporary github repo https://github.com/elser/dbxref that contained just the PO_DBXref.txt file along with its history. I wanted to move it to the Planteome/common-files-for-ref-ontologies repo under Planteome.
<pre>mkdir git_temp
cd git_temp/
git clone https://github.com/elserj/dbxref.git dbxref
cd dbxref/
git remote rm origin
git filter-branch --subdirectory-filter dbxref -- --all
git commit
cd ../
git clone https://github.com/Planteome/common-files-for-ref-ontologies.git common-files-for-ref-ontologies
cd common-files-for-ref-ontologies/
git remote add origin-dbxref ../dbxref
git pull origin-dbxref master
git remote rm origin-dbxref
git push</pre>

Note that not every line is required, noticeably the "git filter-branch", but they may be needed if the repo has multiple folders or other structure that this example didn't have.

Thursday Aug 20th, 2015

2015-08-20T15:19:44Z

Elserj: /* C. Update from IT group- Data Store, AmiGO2- Justin Elser */

=Agenda=
Topic: Planteome Project All Hands Meeting
Time: Aug 20, 2015 8:00 AM (GMT-7:00) Pacific Time (US and Canada)
Join from PC, Mac, iOS or Android: https://zoom.us/j/431144926

* Who: LC, MAL, PJ, AM
* Regrets:

* Link to recording- Video: TBA
* Link to recording- Audio: TBA

== A. General Comments and Updates:==
=== Introductions: ===
* Any new faces Updates on new hires:

== B. Update from Ontologies Working Group:==

== C. Update from IT group- Data Store, AmiGO2- Justin Elser==

=== Migration to github ===
*Seems to be mostly complete. Let me know if there are any more files to transfer with history.

=== AmiGO 2 ===
Fixed annotation loading issue (well, a workaround)
*Working on bisecting issue so we can stay current with Owltools and AmiGO 2 development.

== D. Update from AISO/BisQue group- Justin Preece==

==E. Other Comments:==

==Next meeting Thursday Sept 24th, 2015==

Svn migration to git

2015-08-18T03:12:46Z

Elserj: /* Method if github repo already has files in it */

=Migration of the ontology respository from svn to git=

==Motivation==

After much discussion with Chris Mungall, it was decided to migrate all relevant files from the POC svn repo to a new planteome repository in [github http://github.com].

Not all files are needed to be moved. Most notably, the association files are too large to be hosted on github, so we are looking for a solution for this.

Also, ontology files besides the plant_ontology.obo file were stored in a collaborators_ontology folder. We decided to restructure the repo to make these at the same level

==Dumping the svn repo==

To keep the revision info for the files, we need to dump all of that from svn and then filter it out for the specific files we need to move to git.

On Palea
<pre>cd /data/svnrepos/Poc
svnadmin dump . > /lemma/justin/Poc_svn_migration/Poc_svn_dump
</pre>

This will dump all repo information including revision info and commit messages to a file named Poc_svn_dump. I stored this on lemma as the file is large (>25GB).

===Filtering the dump===
Note: the following was run on one of cluster compute nodes because I didn't want to swamp palea working on it.

I decided to test this out with trait.obo first as a proof of concept. Other files should be similar with changes to the include statement
<pre>cd /lemma/justin/Poc_svn_migration
cat Poc_svn_dump | svndumpfilter include /trunk/ontology/collaborators_ontology/gramene/traits/trait.obo --drop-empty-revs --renumber-revs > trait.obo_filtered_dump
</pre>

The <pre>svndumpfilter</pre> command will go through the dump file and only output revision info for trait.obo, in this case. The full path needs to be in the include argument, otherwise it output an empty repo. The other arguments will reset the revision numbers so that they start at 1 and have no empty revisions.

If the file path needs to be changed, this is the point to do it. Here is a command that I used to change the filename and remove the full path:
<pre>
cat trait.obo_filtered_dump | sed 's/trunk\/ontology\/collaborators_ontology\/gramene\/traits\//plant-trait-ontology.obo/' > trait.obo_filtered_path_fixed_dump
</pre>

==Create a new svn repo to hold the filtered data==
<pre>cd /data/svnrepos
sudo svnadmin create /data/svnrepos/svn2git
sudo chown -R apache: svn2git</pre>

==Copy the filtered dump to the new repo==
Then back on palea (svn server):
<pre>cd /data/svnrepos
sudo svnadmin load ./svn2git < /lemma/justin/Poc_svn_migration/trait.obo_filtered_path_fixed_dump
</pre>

At this point, we should have a fresh clean svn repo with only the filtered files in it with all revision info.

==Copy the svn repo to github==
===Method if repo in github hasn't been created yet (simpler)===
Go to https://import.github.com/new and follow the steps there. This will use the SVN repo created above.

===Method if github repo already has files in it===
I couldn't figure out how to do this direct from the svn, but I figured out how to do it by using an intermediate temporary github repo.

Create a new temporary github repo from the svn using the "simpler" import method described above.

In this example, I created a temporary github repo https://github.com/elser/dbxref that contained just the PO_DBXref.txt file along with its history. I wanted to move it to the Planteome/common-files-for-ref-ontologies repo under Planteome.
<pre>mkdir git_temp
cd git_temp/
git clone https://github.com/elserj/dbxref.git dbxref
cd dbxref/
git remote rm origin
git filter-branch --subdirectory-filter dbxref -- --all
git commit
cd ../
git clone https://github.com/Planteome/common-files-for-ref-ontologies.git common-files-for-ref-ontologies
cd common-files-for-ref-ontologies/
git remote add origin-dbxref ../dbxref
git pull origin-dbxref master
git remote rm origin-dbxref
git push</pre>

Note that not every line is required, noticeably the "git filter-branch", but they may be needed if the repo has multiple folders or other structure that this example didn't have.

Svn migration to git

2015-07-30T22:46:03Z

Elserj: /* Copy the svn repo to github */

=Migration of the ontology respository from svn to git=

==Motivation==

After much discussion with Chris Mungall, it was decided to migrate all relevant files from the POC svn repo to a new planteome repository in [github http://github.com].

Not all files are needed to be moved. Most notably, the association files are too large to be hosted on github, so we are looking for a solution for this.

Also, ontology files besides the plant_ontology.obo file were stored in a collaborators_ontology folder. We decided to restructure the repo to make these at the same level

==Dumping the svn repo==

To keep the revision info for the files, we need to dump all of that from svn and then filter it out for the specific files we need to move to git.

On Palea
<pre>cd /data/svnrepos/Poc
svnadmin dump . > /lemma/justin/Poc_svn_migration/Poc_svn_dump
</pre>

This will dump all repo information including revision info and commit messages to a file named Poc_svn_dump. I stored this on lemma as the file is large (>25GB).

===Filtering the dump===
Note: the following was run on one of cluster compute nodes because I didn't want to swamp palea working on it.

I decided to test this out with trait.obo first as a proof of concept. Other files should be similar with changes to the include statement
<pre>cd /lemma/justin/Poc_svn_migration
cat Poc_svn_dump | svndumpfilter include /trunk/ontology/collaborators_ontology/gramene/traits/trait.obo --drop-empty-revs --renumber-revs > trait.obo_filtered_dump
</pre>

The <pre>svndumpfilter</pre> command will go through the dump file and only output revision info for trait.obo, in this case. The full path needs to be in the include argument, otherwise it output an empty repo. The other arguments will reset the revision numbers so that they start at 1 and have no empty revisions.

If the file path needs to be changed, this is the point to do it. Here is a command that I used to change the filename and remove the full path:
<pre>
cat trait.obo_filtered_dump | sed 's/trunk\/ontology\/collaborators_ontology\/gramene\/traits\//plant-trait-ontology.obo/' > trait.obo_filtered_path_fixed_dump
</pre>

==Create a new svn repo to hold the filtered data==
<pre>cd /data/svnrepos
sudo svnadmin create /data/svnrepos/svn2git
sudo chown -R apache: svn2git</pre>

==Copy the filtered dump to the new repo==
Then back on palea (svn server):
<pre>cd /data/svnrepos
sudo svnadmin load ./svn2git < /lemma/justin/Poc_svn_migration/trait.obo_filtered_path_fixed_dump
</pre>

At this point, we should have a fresh clean svn repo with only the filtered files in it with all revision info.

==Copy the svn repo to github==
===Method if repo in github hasn't been created yet (simpler)===
Go to https://import.github.com/new and follow the steps there. This will use the SVN repo created above.

===Method if github repo already has files in it===
I couldn't figure out how to do this direct from the svn, but I figured out how to do it by using an intermediate temporary github repo.

Create a new temporary github repo from the svn using the "simpler" import method described above.

In this example, I created a temporary github repo https://github.com/elser/dbxref that contained just the PO_DBXref.txt file along with its history. I wanted to move it to the Planteome/common-files-for-ref-ontologies repo under Planteome.
<pre>mkdir git_temp
cd git_temp/
git clone https://github.com/elserj/dbxref.git dbxref
cd dbxref/
git remote rm origin
git filter-branch --subdirectory-filter dbxref -- --all
git commit
cd ../
git clone https://github.com/Planteome/common-files-for-ref-ontologies.git common-files-for-ref-ontologies
cd common-files-for-ref-ontologies/
git remote add origin-dbxref ../dbxref
git pull origin-dbxref
git pull origin-dbxref master
git remote rm origin-dbxref
git push</pre>

Note that not every line is required, noticeably the "git filter-branch", but they may be needed if the repo has multiple folders or other structure that this example didn't have.

Svn migration to git

2015-07-30T22:45:30Z

Elserj:

=Migration of the ontology respository from svn to git=

==Motivation==

After much discussion with Chris Mungall, it was decided to migrate all relevant files from the POC svn repo to a new planteome repository in [github http://github.com].

Not all files are needed to be moved. Most notably, the association files are too large to be hosted on github, so we are looking for a solution for this.

Also, ontology files besides the plant_ontology.obo file were stored in a collaborators_ontology folder. We decided to restructure the repo to make these at the same level

==Dumping the svn repo==

To keep the revision info for the files, we need to dump all of that from svn and then filter it out for the specific files we need to move to git.

On Palea
<pre>cd /data/svnrepos/Poc
svnadmin dump . > /lemma/justin/Poc_svn_migration/Poc_svn_dump
</pre>

This will dump all repo information including revision info and commit messages to a file named Poc_svn_dump. I stored this on lemma as the file is large (>25GB).

===Filtering the dump===
Note: the following was run on one of cluster compute nodes because I didn't want to swamp palea working on it.

I decided to test this out with trait.obo first as a proof of concept. Other files should be similar with changes to the include statement
<pre>cd /lemma/justin/Poc_svn_migration
cat Poc_svn_dump | svndumpfilter include /trunk/ontology/collaborators_ontology/gramene/traits/trait.obo --drop-empty-revs --renumber-revs > trait.obo_filtered_dump
</pre>

The <pre>svndumpfilter</pre> command will go through the dump file and only output revision info for trait.obo, in this case. The full path needs to be in the include argument, otherwise it output an empty repo. The other arguments will reset the revision numbers so that they start at 1 and have no empty revisions.

If the file path needs to be changed, this is the point to do it. Here is a command that I used to change the filename and remove the full path:
<pre>
cat trait.obo_filtered_dump | sed 's/trunk\/ontology\/collaborators_ontology\/gramene\/traits\//plant-trait-ontology.obo/' > trait.obo_filtered_path_fixed_dump
</pre>

==Create a new svn repo to hold the filtered data==
<pre>cd /data/svnrepos
sudo svnadmin create /data/svnrepos/svn2git
sudo chown -R apache: svn2git</pre>

==Copy the filtered dump to the new repo==
Then back on palea (svn server):
<pre>cd /data/svnrepos
sudo svnadmin load ./svn2git < /lemma/justin/Poc_svn_migration/trait.obo_filtered_path_fixed_dump
</pre>

At this point, we should have a fresh clean svn repo with only the filtered files in it with all revision info.

==Copy the svn repo to github==
===Method if repo in github hasn't been created yet (simpler)===
Go to https://import.github.com/new and follow the steps there. This will use the SVN repo created above.

===Method if github repo already has files in it===
I couldn't figure out how to do this direct from the svn, but I figured out how to do it by using an intermediate temporary github repo.

Create a new temporary github repo from the svn using the "simpler" import method described above.

In this example, I created a temporary github repo https://github.com/elser/dbxref that contained just the PO_DBXref.txt file along with its history. I wanted to move it to the Planteome/common-files-for-ref-ontologies repo under Planteome.
<pre>mkdir git_temp
cd git_temp/
git clone https://github.com/elserj/dbxref.git dbxref
cd dbxref/
git remote rm origin
git filter-branch --subdirectory-filter dbxref -- --all
git commit
cd ../
git clone https://github.com/Planteome/common-files-ref-ontologies.git common-files-ref-ontologies
git clone https://github.com/Planteome/common-files-for-ref-ontologies.git common-files-for-ref-ontologies
cd common-files-for-ref-ontologies/
git remote add origin-dbxref ../dbxref
git pull origin-dbxref
git pull origin-dbxref master
git remote rm origin-dbxref
git push</pre>

Note that not every line is required, noticeably the "git filter-branch", but they may be needed if the repo has multiple folders or other structure that this example didn't have.

Svn migration to git

2015-07-30T18:05:33Z

Elserj: /* Copy the filtered dump to the new repo */

Svn migration to git

2015-07-30T00:10:08Z

Elserj: /* Filtering the dump */

=Migration of the ontology respository from svn to git=

==Motivation==

After much discussion with Chris Mungall, it was decided to migrate all relevant files from the POC svn repo to a new planteome repository in [github http://github.com].

Not all files are needed to be moved. Most notably, the association files are too large to be hosted on github, so we are looking for a solution for this.

Also, ontology files besides the plant_ontology.obo file were stored in a collaborators_ontology folder. We decided to restructure the repo to make these at the same level

==Dumping the svn repo==

To keep the revision info for the files, we need to dump all of that from svn and then filter it out for the specific files we need to move to git.

On Palea
<pre>cd /data/svnrepos/Poc
svnadmin dump . > /lemma/justin/Poc_svn_migration/Poc_svn_dump
</pre>

This will dump all repo information including revision info and commit messages to a file named Poc_svn_dump. I stored this on lemma as the file is large (>25GB).

===Filtering the dump===
Note: the following was run on one of cluster compute nodes because I didn't want to swamp palea working on it.

I decided to test this out with trait.obo first as a proof of concept. Other files should be similar with changes to the include statement
<pre>cd /lemma/justin/Poc_svn_migration
cat Poc_svn_dump | svndumpfilter include /trunk/ontology/collaborators_ontology/gramene/traits/trait.obo --drop-empty-revs --renumber-revs > trait.obo_filtered_dump
</pre>

The <pre>svndumpfilter</pre> command will go through the dump file and only output revision info for trait.obo, in this case. The full path needs to be in the include argument, otherwise it output an empty repo. The other arguments will reset the revision numbers so that they start at 1 and have no empty revisions.

If the file path needs to be changed, this is the point to do it. Here is a command that I used to change the filename and remove the full path:
<pre>
cat trait.obo_filtered_dump | sed 's/trunk\/ontology\/collaborators_ontology\/gramene\/traits\//plant-trait-ontology.obo/' > trait.obo_filtered_path_fixed_dump
</pre>

==Create a new svn repo to hold the filtered data==
<pre>cd /data/svnrepos
sudo svnadmin create /data/svnrepos/svn2git
sudo chown -R apache: svn2git</pre>

==Copy the filtered dump to the new repo==
Before we can add the revisions to the repo, we need to at least create the folder where the fitered dump files are in the new repo, or we will get an error:
<pre>cd ~/palea_svn
svn co http://palea.cgrb.oregonstate.edu:/svn/svn2git
cd svn2git
mkdir -p trunk/ontology/collaborators_ontology/gramene/traits
svn add trunk
svn commit --username=elserj
</pre>
Then back on palea (svn server):
<pre>cd /data/svnrepos
sudo svnadmin load ./svn2git < /lemma/justin/Poc_svn_migration/trait.obo_filtered_dump
</pre>

Fix the file path (from the svn client):
<pre>svn up
svn mv trunk/ontology/collaborators_ontology/gramene/traits/trait.obo ./
svn up
svn rm trunk
svn commit</pre>

At this point, we should have a fresh clean svn repo with only the filtered files in it with all revision info.

==Copy the svn repo to github==
Checkout the repo from github

Svn migration to git

2015-07-30T00:03:20Z

Elserj: /* Filtering the dump */

Svn migration to git

2015-07-29T23:39:46Z

Elserj: /* Dumping the svn repo */

AmiGO2 install

2015-07-22T23:27:09Z

Elserj: /* GOLR install: */

== GOLR install: ==
There are a few prerequisites to getting GOLR installed. They appear to be Maven and OwlTools. To install maven, I followed the instructions from here: http://blog.gluster.org/2013/08/yum-install-maven-yes-you-can/, seemed to work without error.

===OWLTools===
Then, to install OWLTools, I did the following:
<pre>
cd /lemma/justin
svn co http://owltools.googlecode.com/svn/trunk/ owltools
</pre>
This creates the owltools directory in my space on lemma.

To compile OWLTools, run:
<pre>
cd OWLTools-Parent
mvn clean package
</pre>
This will take about half an hour.

===SOLR===
Grab the 3.6 version of SOLR from apache and unpack:
<pre>
wget http://archive.apache.org/dist/lucene/solr/3.6.2/apache-solr-3.6.2.tgz
tar zxvf apache-solr-3.6.2.tgz
</pre>

Pull down the latest version of AmiGO:
<pre>
cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

Go back to the SOLR directory and replace the config with those from GOLR:
<pre>
cd /lemma/justin/SOLR/apache-solr-3.6.2/example/solr/conf
cp schema.xml schema.xml.org
cp solrconfig.xml solrconfig.xml.org
cp /data/www/planteome_dev/amigo/golr/solr/conf/s* ./
</pre>

I don't see any edits that need to be made at this point. I think when we move to additional ontologies, we will have to modify schema.xml to account for new relationship types. Cross that bridge when we get there.

Start SOLR(GOLR):
<pre>
cd ../../ (be in the example directory)
java -jar start.jar
</pre>

Now that it seems to be starting up fine, daemonise it so that it runs at a service at boot (Note that any service needs to be okayed by Chris before started):

Add the init.d script as outlined [http://stackoverflow.com/questions/2150767/how-to-start-solr-automatically on this page]

Had to modify that script as follows to make it work on CentOS:

<pre>elserj@palea init.d]$ diff solr solr.org
16,19d15
< # Source function library.
< [ -f /etc/rc.d/init.d/functions ] || exit 0
< . /etc/rc.d/init.d/functions
<
24c20
< daemon "cd /data/www/planteome_dev/SOLR/example; java -jar start.jar &> /var/log/solr/solr.log &"
---
> daemon --chdir='/data/www/plantome_dev/example' --command "java -jar start.jar" --respawn --output=/var/log/solr/solr.log --name=solr --verbose
40c36
< ps -aef | grep start.jar | grep -v grep | awk '{print $2}' | xargs -i++ kill -9 ++
---
> daemon --stop --name=solr --verbose</pre>

At this point, SOLR is now running. Next is to load data to it.

==Load data into GOLR instance==
First we need to pull down the latest AmiGO code from git:
<pre>cd /data/www/planteome_dev
git clone https://github.com/geneontology/amigo.git amigo
</pre>

In the <i>metadata</i> folder are the yaml files that tell owltools how to populate the fields in GOLR

Edit the golr/Makefile to fit our server:
<pre>[elserj@palea golr]$ diff Makefile Makefile.org
18c18
< MAVEN_EXE ?= /usr/bin/mvn
---
> MAVEN_EXE ?= ~/local/src/java/apache-maven-3.0.4/bin/mvn
21c21
< SOLR_URL ?= http://dev.planteome.org:8983/solr
---
> SOLR_URL ?= http://localhost:8080/solr/
24,27c24,27
< OWLTOOLS_ROOT ?= /nfs0/BPP/Jaiswal_Lab/justin/owltools/
< BBOP_JS_ROOT ?= /data/www/planteome_dev/amigo/external/
< #PANTHER_FILES_DIR ?= ~/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/
< #SOLR_DATA_ROOT ?= /srv/solr
---
> OWLTOOLS_ROOT ?= ~/local/src/git/owltools/
> BBOP_JS_ROOT ?= ~/local/src/git/bbop-js/
> PANTHER_FILES_DIR ?= ~/local/src/svn/geneontology.org/trunk/experimental/trees/panther_data/
> SOLR_DATA_ROOT ?= /srv/solr</pre>

===load-ontology===
Try to run the load-ontology part of the Makefile:
<pre>make load-ontology</pre>

This will take some time as it appears to be updating the owltools and then loading the ontologies

At this point, I get an error when trying to load the ontologies. Working with Seth to figure it out.

Errors were mostly caused by memory issues. Had to comment out the ncbitaxon.owl ontology from the list of ones ran. Upped the memory to 20GB on palea. May eventually have to look at running the load on one of the cluster nodes as they have much more RAM. Would have to figure out how to open up the SOLR port to the internal network though.

Now to get annotation test data into GOLR
<pre>make load-test-gaf</pre>
This took a few minutes to run, not long.

At this point, data for an initial test is loaded into SOLR, next is to get AmiGO2 up and running off that instance.

==AmiGO2 install==
Since we already have pulled the amigo code from git, we have to work on configuring it:

<pre>cd amigo/conf
cp .initial_values.yaml amigo.yaml
</pre>

Change the amigo.yaml file as follows:
<pre>[elserj@palea conf]$ diff amigo.yaml .initial_values.yaml
5c5
< value: http://planteome.org/amigo/cgi-bin/crop-amigo
---
> value: http://amigo1.geneontology.org/cgi-bin/amigo
17c17
< value: /data/www/planteome_dev/amigo/perl/bin
---
> value: /home/sjcarbon/local/src/git/amigo/perl/bin
21c21
< value: http://dev.planteome.org
---
> value: http://localhost:9999
33c33
< value: http://dev.planteome.org/solr/
---
> value: http://localhost:8080/solr/
37c37
< value: /data/www/planteome_dev/amigo
---
> value: /home/sjcarbon/local/src/git/amigo
41c41
< value: planteome-dev
---
> value: localhost
45c45
< value: /data/www/planteome_dev/amigo/static
---
> value: /home/sjcarbon/local/src/git/amigo/static
49c49
< value: http://dev.planteome.org/static
---
> value: http://localhost:9999/static
53c53
< value: 'all|[GPTE]O:[u0-9]{7}'
---
> value: 'all|GO:[0-9]{7}'
65c65
< value: /data/www/planteome_dev/amigo/golr_timestamp.log
---
> value: /home/sjcarbon/local/src/git/amigo/golr_timestamp.log
69c69
< value: /data/planteome_dev/amigo/external/bbop.js
---
> value: /home/sjcarbon/local/src/git/amigo/external/bbop.js
73c73
< value: /data/www/planteome_dev/amigo/metadata
---
> value: /home/sjcarbon/local/src/git/amigo/metadata
</pre>

Now to run <pre>make install</pre>

This gives an error about a missing yui-compressor, so need to get that installed.
<pre>
sudo mkdir /usr/local/share/yui-compressor
sudo chown elserj: /usr/local/share/yui-compressor
cd /usr/local/share/yui-compressor
wget https://github.com/downloads/yui/yuicompressor/yuicompressor-2.4.7.zip
unzip yuicompressor-2.4.7.zip
</pre>
Create the following script in /usr/local/bin/yui-comprssor
<pre>
#!/bin/sh
# Quick and dirty front-end script to the yui-compressor that emulates
# /usr/bin/yuicompressor script from Ubuntu release
#
JAVA_HOME=/usr/java/default
YUI_JAR=/usr/local/share/yui-compressor/yuicompressor-2.4.7/build/yuicompressor-2.4.7.jar
# Run YUI Compressor
/usr/bin/java -jar $YUI_JAR "$@"
</pre>
Make it executable with <pre>sudo chmod +x /usr/local/bin/yui-compressor</pre>

Next problem is that rhino gives an error message about "invalid option modules". Still communicating with Seth on solution. Will update when solution found.

Solution was to comment out the test and docs part of the install target in the Makefile. Rhino was apparently only used for unit testing, which we don't really need to do.

===Configure Apache2===

The Apache config file needs to be modified
<pre>
[elserj@palea amigo]$ diff amigo2-apache-local.conf conf/amigo2-apache.conf
2,4c2,3
< <VirtualHost *:80>
< ServerAdmin elserj@science.oregonstate.edu
< ServerName dev.planteome.org
---
> <VirtualHost *:9999>
> ServerAdmin sjcarbon@localhost
8c7
< DocumentRoot /data/www/planteome_dev/amigo
---
> DocumentRoot /home/sjcarbon/local/src/git/amigo
11c10
< <Directory /data/www/planteome_dev/amigo/static>
---
> <Directory /home/sjcarbon/local/src/git/amigo/static>
20c19
< ScriptAlias /$binnm /data/www/planteome_dev/amigo/perl/bin/$binnm
---
> ScriptAlias /$binnm /home/sjcarbon/local/src/git/amigo/perl/bin/$binnm
48,59c47,48
<
< ProxyRequests Off
< <Proxy *>
< Order deny,allow
< Allow from 192.168.1.52
< </Proxy>
<
< ProxyPass /solr http://localhost:8983/solr
< ProxyPassReverse /solr http://localhost:8983/solr
<
< ErrorLog /data/www/planteome_dev/amigo/log/error.log
< ScriptLog /data/www/planteome_dev/amigo/log/cgi.log
---
> ErrorLog /var/log/apache2/error.log
> ScriptLog /var/log/apache2/cgi.log
65c54
< CustomLog /data/www/planteome_dev/amigo/log/access.log combined
---
> CustomLog /var/log/apache2/access.log combined</pre>

For this to work, the mod_macro module for Apache must be installed. I found it as a downloadable rpm, so I installed it that way:
<pre>ftp://ftp.pbone.net/mirror/ftp.pramberger.at/systems/linux/contrib/rhel6/x86_64/mod_macro-1.1.11-2.el6.pp.x86_64.rpm
sudo rpm -Uvih mod_macro-1.1.11-2.el6.pp.x86_64.rpm</pre>

The proxy settings are to make it so the Server is able to talk to the SOLR data.

I changed the /etc/httpd/conf/httpd.conf file to have the following line for the dev.planteome.org section
<pre>Include /data/www/planteome_dev/amigo/amigo2-apache-local.conf</pre>
Note that this cannot go in it's own VirtualHost section as it will error because of a VirtualHost inside a VirtualHost

doing the <pre>make install</pre> now works without error.

However, the server doesn't work when navigated to. It looks like a perl module is missing. Installed the following via cpan:
<pre>CGI::Application::Plugin::Forward</pre>

Error is now about "Type of arg 1 to keys must be hash" Will work on this error.

This error apparently is the result of the older version of perl that we have installed. Seth fixed this in git, so I did a git pull and got past it.

However, another perl module needed to be installed via cpan:
<pre>CGI::Application::Dispatch</pre>

At this point Amigo2 appears to be working.

'''This page will be updated as I progress.'''

Wednesday June 24th, 2015

2015-06-23T23:20:28Z

Elserj: /* B. Update from IT group- Data Store, AmiGO2- Justin Elser */

=Agenda=
Planteome Project is inviting you to a scheduled Zoom meeting.
Join from PC, Mac, iOS or Android: https://zoom.us/j/667957473

* Who: LC, MAL, PJ, JP,
* Not available:
(Others: GG, JE, DWS, EZ, ST? )

== A. General Comments and Updates:==
=== Introductions: ===
* Any new faces?
===Updates on new hires===
* New postdoc at OSU: details TBA
===Workshop and travels: Elizabeth's questions===

a. What will be the objective of the workshop?

b. Who will be the attendees ? data manager, ontology curators, researchers?

I propose to consider: Use of Protégé; Discussion on Traits/trait mapping; Discussion on possible annotation pipelines and test on data sets

c. Travel budget: shall we keep our travel budget for this workshop or can we use it entirely for visit to CGIAR centers on our side

== B. Update from IT group- Data Store, AmiGO2- Justin Elser==

* AmiGO 2 progress
** Fixed issue with loading both EO and TO together. Issue was that they were both trying to use the "TEMP" namespace after the conversion to OWL. Wrote a little script to fix it.
** Wrote an importer owl file (planteome.owl) that is used when loading. We can add new ontologies simply by adding a line to the import list.

* Git migration
** Working on using Chris Mungall's [https://github.com/cmungall/gosf2github/ script] to migrate TO term requests from sourceforge to github.

== C. Update from AISO/BisQue group- Justin Preece:==

== D. Update from Ontologies Working Group:==

==E. Other Comments:==

==Next meeting Thursday July 23rd, 2015==

Wednesday June 24th, 2015

2015-06-23T23:17:03Z

Elserj: /* B. Update from IT group- Data Store, AmiGO2- Justin Elser */

=Agenda=
Planteome Project is inviting you to a scheduled Zoom meeting.
Join from PC, Mac, iOS or Android: https://zoom.us/j/667957473

* Who: LC, MAL, PJ, JP,
* Not available:
(Others: GG, JE, DWS, EZ, ST? )

== A. General Comments and Updates:==
=== Introductions: ===
* Any new faces?
===Updates on new hires===
* New postdoc at OSU: details TBA
===Workshop and travels: Elizabeth's questions===

a. What will be the objective of the workshop?

b. Who will be the attendees ? data manager, ontology curators, researchers?

I propose to consider: Use of Protégé; Discussion on Traits/trait mapping; Discussion on possible annotation pipelines and test on data sets

c. Travel budget: shall we keep our travel budget for this workshop or can we use it entirely for visit to CGIAR centers on our side

== B. Update from IT group- Data Store, AmiGO2- Justin Elser==

* AmiGO 2 progress
** Fixed issue with loading both EO and TO together. Issue was that they were both trying to use the "TEMP" namespace after the conversion to OWL. Wrote a little script to fix it.
** Wrote an importer owl file (planteome.owl) that is used when loading. We can add new ontologies simply by adding a line to the import list.

* Git migration
** Working on using Chris Mungall's script to migrate TO term requests from sourceforge to github.

== C. Update from AISO/BisQue group- Justin Preece:==

== D. Update from Ontologies Working Group:==

==E. Other Comments:==

==Next meeting Thursday July 23rd, 2015==

Data storage and AmiGO2 Working Group

2015-05-27T23:29:13Z

Elserj:

=Goals and Objectives:=
== Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes. ==
*Deliverables: A centralized portal for common reference ontologies for plants and the associated data sets. Novel data store and web user interface.
===3.1 Planteome Web Portal Development===
* Drupal portal will host the AmiGO browser, the ontology database (similar to the one developed by the PO and the GO), and a BioMart
* Transition to AmiGO 2.0 with new features

===3.2 Planteome Data Warehouse Development===
* Novel data warehouse for storing both the ontologies and annotation data based on [http://nosql-database.org/ NoSQL] (e.g. MongoDB, http://www.mongodb.org, and Apache™ Hadoop®, http://hadoop.apache.org)
* Integrate the MapReduce algorithm to increase scalability and performance
* Investigate using HDF ([http://en.wikipedia.org/wiki/Hierarchical_Data_Format Hierarchical Data Format]), as a storage format for any numerical or sequence-based data.
* Create an efficient way to add annotations incrementally to the database, (not possible in the current AmiGO database)
* Implementation of OLAP (Online Analytical Processing) data cubes (http://en.wikipedia.org/wiki/OLAP_cube)

===3.3 Integration with the iPlant infrastructure ===
* Initial design and testing will happen locally at the Center for Genome Research and Biocomputing at Oregon State University
* Use of virtual machine (VM) images in the iPlant cloud computing environments
* Utilization of high performance computing resources, such as:
** The supercomputer 'Stampede' at Texas Advanced Computing Center (TACC)
** Use of iRODS at iPlant for data file storage and retrieval
** Image hosting via Bisque hosted on the iPlant infrastructure (See 3.4, below)
* Interaction with resources such as CoGE, Bisque, and the Integrated Breeding Platform (IBP)

===3.4 Library of Publicly-Accessible, Annotated Digital Images===
* Design a relational data schema to support the large-scale storage of annotated images (and their associated metadata)
* Image library main goal: A training set for a new auto-segmentation and annotation active-learning algorithm
* Support other visual analysis tools and the integration of image data with ontology data
* Will also function as a home for community-contributed image data

===3.5 Application Programming Interface (APIs)===
* Develop of publicly available APIs for both internal and external data access to ontology terms and annotations
* Extend the existing lightweight web services providing Plant Ontology terms, synonyms, and definitions to the Planteoem APIs, including direct web service access to annotated data
* Potential Users:
** Gramene project- information about annotations and ontologies
** DOE KBase project (http://kbase.science.energy.gov/)
** iPlant tools and services.

* Integrate our data with other external APIs, For example:
** EBI (the Gene Expression Atlas, Ensembl Plants, IntAct),
** ERA-CAPS (genotype-to-phenotype data)
** DOE KBase
** GCP Integrated Breeding Platform
** Agave on iPlant which provides web-focused developer access to the iPlant data store and other integration services, providing a direct link to high-performance computing systems such as the TACC.

=Participants=
* Jaiswal Lab (OSU, BPP): Justin Elser
* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon
* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)

=Data storage and AmiGO 2 Working Group Meetings:=
==Data storage and AmiGO 2 call 1-30-15==
* Who: PJ, CM, Seth, EZ, LC, JP, JE
* Discussion of the planned transition to the AmiGO 2.0 platform
* JE is working on installing SolR database - View details and progress reports here: [[AmiGO2_install]]

== Data Storage and AmiGO2 call 2-18-15==
* Who: JE, JP, EZ
* Link to video recording: [[Media:Data_Storage_2-18-15.mp4]]
* Link to audio recording: [[File:Data Storage Meeting audio only 2-18-15.m4a|thumbnail|Data_Storage_Meeting_audio_only_2-18-15.m4a]]

* Further discussion of AmiGO2 progress and overview of AmiGO2 interface

== Planteome Interface meeting 3-2-15==
Who: EZ, LC, JE, PJ ...??
* Link to video recording: [[File:Planteome Interface mtg video 3-2-15.mp4|thumbnail|Planteome_Interface_mtg_video_3-2-15.mp4]]
* Link to audio recording: [[File:Planteome Interface mtg audio 3-2-15.m4a|thumbnail|Planteome Interface mtg audio 3-2-15.m4a]]

* EZ: First thing: focus of the project, speed up queries, data visualization, data organization
* User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
* Amigo 2, could build enhanced interface so users could inspect their data and build queries.
* what functionalities are needed?
* Questions:
**How will the users access the interface?
** How will they use the interface?
===Involvement of other organisms? e.g. viruses, animals, etc===
* Could the tools be expanded to other organisms
* Crops are interacting with the environment, other organisms
=== AmiGO2 introduction===
* show filtered image
* Cytoscape Sif file, ontology network
* bring in other ontologies, Rice Xanthomanas example
* ontology formats

==Data storage and AmiGO2 Working Group Meeting 4-16-15==

Who: EZ, BQ, PJ, JP, LC, JE

* Link to video recording: [[File:Data_storage_and_AmiGO2_video_4-16_15.mp4|thumbnail|Data_storage_and_AmiGO2_video_4-16_15.mp4]]
* Link to audio recording: [[File:Data storage and AmiGO2 audio 4-16 15.m4a|thumbnail|Data storage and AmiGO2 audio 4-16 15.m4a]]

* Introductions

* Storing code developed on Planteome project on Github

* posting notes on wiki
* data visualization aspect within AmiGO2- work with JE on
* Data annotation- wikipedia style?
* different levels of access
* To do: Send link to Eugene and Botong- circulate the developer position ad

==Relevant links:==
* https://github.com/geneontology/amigo
* Demo: http://amigo.geneontology.org/
* http://amigo2.berkeleybop.org/ - dev server

==Data storage and AmiGO2 Working Group meeting 5-1-15==
Who: PJ, BQ, EZ, CM, JE
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]
* Link to audio: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]

===Demo of GO enrichment tool===
*At the GO website (www.geneontology.org)
*See how it works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.

*Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
* Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
*Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.
This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.

I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.

BinGO
http://bioinformatics.oxfordjournals.org/content/21/16/3448.full
AgriGO
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/

==Data storage and AmiGO2 Working Group Meeting 5-15-15==
Who: PJ, EZ, BQ, JE, CM

*Continue to show how the enrichment analysis tools work(agriGO).
*Discuss about the language and character problem on the page.
*Agreed to start with design the requirement specification.
*Share the old database scheme with EZ and BQ.
*Show the Annotation database to EZ and BQ (unfinished, need to be continued).

EZ and BQ will start with analyzing the old database scheme and try to study the enrichment analysis algorithms, the first goal of the group is to show the search result through tables. The next step will be visualize it with Graph.

==Data storage and visualization Working Group Meeting 5-27-15==
Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)

Link to recordings (in 2 parts):
Audio P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a|thumbnail|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]

Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4|thumbnail|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]

Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a|thumbnail|Data_Visualization_5-27-15_audio.m4a]]

Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4|thumbnail|Data_Visualization_5-27-15_part_2.mp4]]

* Explanation of ontologies to new students
* Overview of older AmiGO browser
* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php
* Used gene set from above to show AgriGO usage

Data storage and AmiGO2 Working Group

2015-05-27T23:28:22Z

Elserj:

=Goals and Objectives:=
== Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes. ==
*Deliverables: A centralized portal for common reference ontologies for plants and the associated data sets. Novel data store and web user interface.
===3.1 Planteome Web Portal Development===
* Drupal portal will host the AmiGO browser, the ontology database (similar to the one developed by the PO and the GO), and a BioMart
* Transition to AmiGO 2.0 with new features

===3.2 Planteome Data Warehouse Development===
* Novel data warehouse for storing both the ontologies and annotation data based on [http://nosql-database.org/ NoSQL] (e.g. MongoDB, http://www.mongodb.org, and Apache™ Hadoop®, http://hadoop.apache.org)
* Integrate the MapReduce algorithm to increase scalability and performance
* Investigate using HDF ([http://en.wikipedia.org/wiki/Hierarchical_Data_Format Hierarchical Data Format]), as a storage format for any numerical or sequence-based data.
* Create an efficient way to add annotations incrementally to the database, (not possible in the current AmiGO database)
* Implementation of OLAP (Online Analytical Processing) data cubes (http://en.wikipedia.org/wiki/OLAP_cube)

===3.3 Integration with the iPlant infrastructure ===
* Initial design and testing will happen locally at the Center for Genome Research and Biocomputing at Oregon State University
* Use of virtual machine (VM) images in the iPlant cloud computing environments
* Utilization of high performance computing resources, such as:
** The supercomputer 'Stampede' at Texas Advanced Computing Center (TACC)
** Use of iRODS at iPlant for data file storage and retrieval
** Image hosting via Bisque hosted on the iPlant infrastructure (See 3.4, below)
* Interaction with resources such as CoGE, Bisque, and the Integrated Breeding Platform (IBP)

===3.4 Library of Publicly-Accessible, Annotated Digital Images===
* Design a relational data schema to support the large-scale storage of annotated images (and their associated metadata)
* Image library main goal: A training set for a new auto-segmentation and annotation active-learning algorithm
* Support other visual analysis tools and the integration of image data with ontology data
* Will also function as a home for community-contributed image data

===3.5 Application Programming Interface (APIs)===
* Develop of publicly available APIs for both internal and external data access to ontology terms and annotations
* Extend the existing lightweight web services providing Plant Ontology terms, synonyms, and definitions to the Planteoem APIs, including direct web service access to annotated data
* Potential Users:
** Gramene project- information about annotations and ontologies
** DOE KBase project (http://kbase.science.energy.gov/)
** iPlant tools and services.

* Integrate our data with other external APIs, For example:
** EBI (the Gene Expression Atlas, Ensembl Plants, IntAct),
** ERA-CAPS (genotype-to-phenotype data)
** DOE KBase
** GCP Integrated Breeding Platform
** Agave on iPlant which provides web-focused developer access to the iPlant data store and other integration services, providing a direct link to high-performance computing systems such as the TACC.

=Participants=
* Jaiswal Lab (OSU, BPP): Justin Elser
* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon
* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)

=Data storage and AmiGO 2 Working Group Meetings:=
==Data storage and AmiGO 2 call 1-30-15==
* Who: PJ, CM, Seth, EZ, LC, JP, JE
* Discussion of the planned transition to the AmiGO 2.0 platform
* JE is working on installing SolR database - View details and progress reports here: [[AmiGO2_install]]

== Data Storage and AmiGO2 call 2-18-15==
* Who: JE, JP, EZ
* Link to video recording: [[Media:Data_Storage_2-18-15.mp4]]
* Link to audio recording: [[File:Data Storage Meeting audio only 2-18-15.m4a|thumbnail|Data_Storage_Meeting_audio_only_2-18-15.m4a]]

* Further discussion of AmiGO2 progress and overview of AmiGO2 interface

== Planteome Interface meeting 3-2-15==
Who: EZ, LC, JE, PJ ...??
* Link to video recording: [[File:Planteome Interface mtg video 3-2-15.mp4|thumbnail|Planteome_Interface_mtg_video_3-2-15.mp4]]
* Link to audio recording: [[File:Planteome Interface mtg audio 3-2-15.m4a|thumbnail|Planteome Interface mtg audio 3-2-15.m4a]]

* EZ: First thing: focus of the project, speed up queries, data visualization, data organization
* User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
* Amigo 2, could build enhanced interface so users could inspect their data and build queries.
* what functionalities are needed?
* Questions:
**How will the users access the interface?
** How will they use the interface?
===Involvement of other organisms? e.g. viruses, animals, etc===
* Could the tools be expanded to other organisms
* Crops are interacting with the environment, other organisms
=== AmiGO2 introduction===
* show filtered image
* Cytoscape Sif file, ontology network
* bring in other ontologies, Rice Xanthomanas example
* ontology formats

==Data storage and AmiGO2 Working Group Meeting 4-16-15==

Who: EZ, BQ, PJ, JP, LC, JE

* Link to video recording: [[File:Data_storage_and_AmiGO2_video_4-16_15.mp4|thumbnail|Data_storage_and_AmiGO2_video_4-16_15.mp4]]
* Link to audio recording: [[File:Data storage and AmiGO2 audio 4-16 15.m4a|thumbnail|Data storage and AmiGO2 audio 4-16 15.m4a]]

* Introductions

* Storing code developed on Planteome project on Github

* posting notes on wiki
* data visualization aspect within AmiGO2- work with JE on
* Data annotation- wikipedia style?
* different levels of access
* To do: Send link to Eugene and Botong- circulate the developer position ad

==Relevant links:==
* https://github.com/geneontology/amigo
* Demo: http://amigo.geneontology.org/
* http://amigo2.berkeleybop.org/ - dev server

==Data storage and AmiGO2 Working Group meeting 5-1-15==
Who: PJ, BQ, EZ, CM, JE
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]

===Demo of GO enrichment tool===
*At the GO website (www.geneontology.org)
*See how it works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.

*Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
* Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
*Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.
This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.

I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.

BinGO
http://bioinformatics.oxfordjournals.org/content/21/16/3448.full
AgriGO
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/

==Data storage and AmiGO2 Working Group Meeting 5-15-15==
Who: PJ, EZ, BQ, JE, CM

*Continue to show how the enrichment analysis tools work(agriGO).
*Discuss about the language and character problem on the page.
*Agreed to start with design the requirement specification.
*Share the old database scheme with EZ and BQ.
*Show the Annotation database to EZ and BQ (unfinished, need to be continued).

EZ and BQ will start with analyzing the old database scheme and try to study the enrichment analysis algorithms, the first goal of the group is to show the search result through tables. The next step will be visualize it with Graph.

==Data storage and visualization Working Group Meeting 5-27-15==
Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)

Link to recordings (in 2 parts):
Audio P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a|thumbnail|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]

Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4|thumbnail|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]

Audio P.2: [[File:Data_Visualization_5-27-15_audio.m4a|thumbnail|Data_Visualization_5-27-15_audio.m4a]]

Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4|thumbnail|Data_Visualization_5-27-15_part_2.mp4]]

* Explanation of ontologies to new students
* Overview of older AmiGO browser
* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php
* Used gene set from above to show AgriGO usage

File:Data Visualization 5-27-15 audio.m4a

2015-05-27T23:27:36Z

Elserj:

Data storage and AmiGO2 Working Group

2015-05-27T23:26:23Z

Elserj:

=Goals and Objectives:=
== Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes. ==
*Deliverables: A centralized portal for common reference ontologies for plants and the associated data sets. Novel data store and web user interface.
===3.1 Planteome Web Portal Development===
* Drupal portal will host the AmiGO browser, the ontology database (similar to the one developed by the PO and the GO), and a BioMart
* Transition to AmiGO 2.0 with new features

===3.2 Planteome Data Warehouse Development===
* Novel data warehouse for storing both the ontologies and annotation data based on [http://nosql-database.org/ NoSQL] (e.g. MongoDB, http://www.mongodb.org, and Apache™ Hadoop®, http://hadoop.apache.org)
* Integrate the MapReduce algorithm to increase scalability and performance
* Investigate using HDF ([http://en.wikipedia.org/wiki/Hierarchical_Data_Format Hierarchical Data Format]), as a storage format for any numerical or sequence-based data.
* Create an efficient way to add annotations incrementally to the database, (not possible in the current AmiGO database)
* Implementation of OLAP (Online Analytical Processing) data cubes (http://en.wikipedia.org/wiki/OLAP_cube)

===3.3 Integration with the iPlant infrastructure ===
* Initial design and testing will happen locally at the Center for Genome Research and Biocomputing at Oregon State University
* Use of virtual machine (VM) images in the iPlant cloud computing environments
* Utilization of high performance computing resources, such as:
** The supercomputer 'Stampede' at Texas Advanced Computing Center (TACC)
** Use of iRODS at iPlant for data file storage and retrieval
** Image hosting via Bisque hosted on the iPlant infrastructure (See 3.4, below)
* Interaction with resources such as CoGE, Bisque, and the Integrated Breeding Platform (IBP)

===3.4 Library of Publicly-Accessible, Annotated Digital Images===
* Design a relational data schema to support the large-scale storage of annotated images (and their associated metadata)
* Image library main goal: A training set for a new auto-segmentation and annotation active-learning algorithm
* Support other visual analysis tools and the integration of image data with ontology data
* Will also function as a home for community-contributed image data

===3.5 Application Programming Interface (APIs)===
* Develop of publicly available APIs for both internal and external data access to ontology terms and annotations
* Extend the existing lightweight web services providing Plant Ontology terms, synonyms, and definitions to the Planteoem APIs, including direct web service access to annotated data
* Potential Users:
** Gramene project- information about annotations and ontologies
** DOE KBase project (http://kbase.science.energy.gov/)
** iPlant tools and services.

* Integrate our data with other external APIs, For example:
** EBI (the Gene Expression Atlas, Ensembl Plants, IntAct),
** ERA-CAPS (genotype-to-phenotype data)
** DOE KBase
** GCP Integrated Breeding Platform
** Agave on iPlant which provides web-focused developer access to the iPlant data store and other integration services, providing a direct link to high-performance computing systems such as the TACC.

=Participants=
* Jaiswal Lab (OSU, BPP): Justin Elser
* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon
* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)

=Data storage and AmiGO 2 Working Group Meetings:=
==Data storage and AmiGO 2 call 1-30-15==
* Who: PJ, CM, Seth, EZ, LC, JP, JE
* Discussion of the planned transition to the AmiGO 2.0 platform
* JE is working on installing SolR database - View details and progress reports here: [[AmiGO2_install]]

== Data Storage and AmiGO2 call 2-18-15==
* Who: JE, JP, EZ
* Link to video recording: [[Media:Data_Storage_2-18-15.mp4]]
* Link to audio recording: [[File:Data Storage Meeting audio only 2-18-15.m4a|thumbnail|Data_Storage_Meeting_audio_only_2-18-15.m4a]]

* Further discussion of AmiGO2 progress and overview of AmiGO2 interface

== Planteome Interface meeting 3-2-15==
Who: EZ, LC, JE, PJ ...??
* Link to video recording: [[File:Planteome Interface mtg video 3-2-15.mp4|thumbnail|Planteome_Interface_mtg_video_3-2-15.mp4]]
* Link to audio recording: [[File:Planteome Interface mtg audio 3-2-15.m4a|thumbnail|Planteome Interface mtg audio 3-2-15.m4a]]

* EZ: First thing: focus of the project, speed up queries, data visualization, data organization
* User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
* Amigo 2, could build enhanced interface so users could inspect their data and build queries.
* what functionalities are needed?
* Questions:
**How will the users access the interface?
** How will they use the interface?
===Involvement of other organisms? e.g. viruses, animals, etc===
* Could the tools be expanded to other organisms
* Crops are interacting with the environment, other organisms
=== AmiGO2 introduction===
* show filtered image
* Cytoscape Sif file, ontology network
* bring in other ontologies, Rice Xanthomanas example
* ontology formats

==Data storage and AmiGO2 Working Group Meeting 4-16-15==

Who: EZ, BQ, PJ, JP, LC, JE

* Link to video recording: [[File:Data_storage_and_AmiGO2_video_4-16_15.mp4|thumbnail|Data_storage_and_AmiGO2_video_4-16_15.mp4]]
* Link to audio recording: [[File:Data storage and AmiGO2 audio 4-16 15.m4a|thumbnail|Data storage and AmiGO2 audio 4-16 15.m4a]]

* Introductions

* Storing code developed on Planteome project on Github

* posting notes on wiki
* data visualization aspect within AmiGO2- work with JE on
* Data annotation- wikipedia style?
* different levels of access
* To do: Send link to Eugene and Botong- circulate the developer position ad

==Relevant links:==
* https://github.com/geneontology/amigo
* Demo: http://amigo.geneontology.org/
* http://amigo2.berkeleybop.org/ - dev server

==Data storage and AmiGO2 Working Group meeting 5-1-15==
Who: PJ, BQ, EZ, CM, JE
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]

===Demo of GO enrichment tool===
*At the GO website (www.geneontology.org)
*See how it works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.

*Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
* Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
*Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.
This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.

I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.

BinGO
http://bioinformatics.oxfordjournals.org/content/21/16/3448.full
AgriGO
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/

==Data storage and AmiGO2 Working Group Meeting 5-15-15==
Who: PJ, EZ, BQ, JE, CM

*Continue to show how the enrichment analysis tools work(agriGO).
*Discuss about the language and character problem on the page.
*Agreed to start with design the requirement specification.
*Share the old database scheme with EZ and BQ.
*Show the Annotation database to EZ and BQ (unfinished, need to be continued).

EZ and BQ will start with analyzing the old database scheme and try to study the enrichment analysis algorithms, the first goal of the group is to show the search result through tables. The next step will be visualize it with Graph.

==Data storage and visualization Working Group Meeting 5-27-15==
Who: PJ, EZ, BQ, JE, LC, 2 REU students (Christian and Marquis)

Link to recordings (in 2 parts):
Audio P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-audio only.m4a|thumbnail|Planteome_Data_Vis_Mtg_p1_5-27-15-audio_only.m4a]]

Video P.1: [[File:Planteome Data Vis Mtg p1 5-27-15-video.mp4|thumbnail|Planteome Data Vis Mtg p1 5-27-15-video.mp4]]

Video P.2: [[File:Data_Visualization_5-27-15_part_2.mp4|thumbnail|Data_Visualization_5-27-15_part_2.mp4]]

* Explanation of ontologies to new students
* Overview of older AmiGO browser
* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php
* Used gene set from above to show AgriGO usage

File:Data Visualization 5-27-15 part 2.mp4

2015-05-27T23:24:14Z

Elserj: Part 2 of the Zoom conference call for the Data Visualization and Storage Working group. Recorded 5/27/15

Part 2 of the Zoom conference call for the Data Visualization and Storage Working group. Recorded 5/27/15

Data storage and AmiGO2 Working Group

2015-05-27T19:19:44Z

Elserj:

=Goals and Objectives:=
== Aim-3: Develop an online informatics portal and data warehouse for ontology-based, annotated plant genome data and plant genomes. ==
*Deliverables: A centralized portal for common reference ontologies for plants and the associated data sets. Novel data store and web user interface.
===3.1 Planteome Web Portal Development===
* Drupal portal will host the AmiGO browser, the ontology database (similar to the one developed by the PO and the GO), and a BioMart
* Transition to AmiGO 2.0 with new features

===3.2 Planteome Data Warehouse Development===
* Novel data warehouse for storing both the ontologies and annotation data based on [http://nosql-database.org/ NoSQL] (e.g. MongoDB, http://www.mongodb.org, and Apache™ Hadoop®, http://hadoop.apache.org)
* Integrate the MapReduce algorithm to increase scalability and performance
* Investigate using HDF ([http://en.wikipedia.org/wiki/Hierarchical_Data_Format Hierarchical Data Format]), as a storage format for any numerical or sequence-based data.
* Create an efficient way to add annotations incrementally to the database, (not possible in the current AmiGO database)
* Implementation of OLAP (Online Analytical Processing) data cubes (http://en.wikipedia.org/wiki/OLAP_cube)

===3.3 Integration with the iPlant infrastructure ===
* Initial design and testing will happen locally at the Center for Genome Research and Biocomputing at Oregon State University
* Use of virtual machine (VM) images in the iPlant cloud computing environments
* Utilization of high performance computing resources, such as:
** The supercomputer 'Stampede' at Texas Advanced Computing Center (TACC)
** Use of iRODS at iPlant for data file storage and retrieval
** Image hosting via Bisque hosted on the iPlant infrastructure (See 3.4, below)
* Interaction with resources such as CoGE, Bisque, and the Integrated Breeding Platform (IBP)

===3.4 Library of Publicly-Accessible, Annotated Digital Images===
* Design a relational data schema to support the large-scale storage of annotated images (and their associated metadata)
* Image library main goal: A training set for a new auto-segmentation and annotation active-learning algorithm
* Support other visual analysis tools and the integration of image data with ontology data
* Will also function as a home for community-contributed image data

===3.5 Application Programming Interface (APIs)===
* Develop of publicly available APIs for both internal and external data access to ontology terms and annotations
* Extend the existing lightweight web services providing Plant Ontology terms, synonyms, and definitions to the Planteoem APIs, including direct web service access to annotated data
* Potential Users:
** Gramene project- information about annotations and ontologies
** DOE KBase project (http://kbase.science.energy.gov/)
** iPlant tools and services.

* Integrate our data with other external APIs, For example:
** EBI (the Gene Expression Atlas, Ensembl Plants, IntAct),
** ERA-CAPS (genotype-to-phenotype data)
** DOE KBase
** GCP Integrated Breeding Platform
** Agave on iPlant which provides web-focused developer access to the iPlant data store and other integration services, providing a direct link to high-performance computing systems such as the TACC.

=Participants=
* Jaiswal Lab (OSU, BPP): Justin Elser
* Mungall Group (Lawrence Berkeley National Laboratory): Chris Mungall (Co-PI), Seth Carbon
* Zhang Lab (OSU, EECS):'' Eugene Zhang (Co-PI), Botong Qu (CS Ph.D. student)

=Data storage and AmiGO 2 Working Group Meetings:=
==Data storage and AmiGO 2 call 1-30-15==
* Who: PJ, CM, Seth, EZ, LC, JP, JE
* Discussion of the planned transition to the AmiGO 2.0 platform
* JE is working on installing SolR database - View details and progress reports here: [[AmiGO2_install]]

== Data Storage and AmiGO2 call 2-18-15==
* Who: JE, JP, EZ
* Link to video recording: [[Media:Data_Storage_2-18-15.mp4]]
* Link to audio recording: [[File:Data Storage Meeting audio only 2-18-15.m4a|thumbnail|Data_Storage_Meeting_audio_only_2-18-15.m4a]]

* Further discussion of AmiGO2 progress and overview of AmiGO2 interface

== Planteome Interface meeting 3-2-15==
Who: EZ, LC, JE, PJ ...??
* Link to video recording: [[File:Planteome Interface mtg video 3-2-15.mp4|thumbnail|Planteome_Interface_mtg_video_3-2-15.mp4]]
* Link to audio recording: [[File:Planteome Interface mtg audio 3-2-15.m4a|thumbnail|Planteome Interface mtg audio 3-2-15.m4a]]

* EZ: First thing: focus of the project, speed up queries, data visualization, data organization
* User Interface: it would be good to see how the users operate and what kinds of questions they would ask.
* Amigo 2, could build enhanced interface so users could inspect their data and build queries.
* what functionalities are needed?
* Questions:
**How will the users access the interface?
** How will they use the interface?
===Involvement of other organisms? e.g. viruses, animals, etc===
* Could the tools be expanded to other organisms
* Crops are interacting with the environment, other organisms
=== AmiGO2 introduction===
* show filtered image
* Cytoscape Sif file, ontology network
* bring in other ontologies, Rice Xanthomanas example
* ontology formats

==Data storage and AmiGO2 Working Group Meeting 4-16-15==

Who: EZ, BQ, PJ, JP, LC, JE

* Link to video recording: [[File:Data_storage_and_AmiGO2_video_4-16_15.mp4|thumbnail|Data_storage_and_AmiGO2_video_4-16_15.mp4]]
* Link to audio recording: [[File:Data storage and AmiGO2 audio 4-16 15.m4a|thumbnail|Data storage and AmiGO2 audio 4-16 15.m4a]]

* Introductions

* Storing code developed on Planteome project on Github

* posting notes on wiki
* data visualization aspect within AmiGO2- work with JE on
* Data annotation- wikipedia style?
* different levels of access
* To do: Send link to Eugene and Botong- circulate the developer position ad

==Relevant links:==
* https://github.com/geneontology/amigo
* Demo: http://amigo.geneontology.org/
* http://amigo2.berkeleybop.org/ - dev server

==Data storage and AmiGO2 Working Group meeting 5-1-15==
Who: PJ, BQ, EZ, CM, JE
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-video.mp4|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-video.mp4]]
* Link to video: [[File:Data Storage + AmiGO2 meeting 5-1-15-audio.m4a|thumbnail|Data Storage + AmiGO2 meeting 5-1-15-audio.m4a]]

===Demo of GO enrichment tool===
*At the GO website (www.geneontology.org)
*See how it works there compared to the one at AGRIGO (http://bioinfo.cau.edu.cn/agriGO/analysis.php). See if your NIH proposal work with Yanmin Di overlaps and can be adopted.

*Set of genes you can get a list of Arabidopsis thaliana genes from the attached file. (email)
* Gene pages at Gramene e.g. http://archive.gramene.org/db/genes/search_gene?acc=GR:0101175 or elsewhere
*Start thinking about building a gene database, with different access levels for admins and curators, limited in what fields are allowed to be edited by what level.
This is for building the community gene annotation tools. The annotated data from this database can be synced with the AmiGOdb version that Justin Elser and Chris are working on.

I hope this will give Bo, enough width to work until the AMIGO build and datasets mature.

BinGO
http://bioinformatics.oxfordjournals.org/content/21/16/3448.full
AgriGO
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896167/

==Data storage and AmiGO2 Working Group Meeting 5-15-15==
Who: PJ, EZ, BQ, JE, CM

*Continue to show how the enrichment analysis tools work(agriGO).
*Discuss about the language and character problem on the page.
*Agreed to start with design the requirement specification.
*Share the old database scheme with EZ and BQ.
*Show the Annotation database to EZ and BQ (unfinished, need to be continued).

EZ and BQ will start with analyzing the old database scheme and try to study the enrichment analysis algorithms, the first goal of the group is to show the search result through tables. The next step will be visualize it with Graph.

==Data storage and visualization Working Group Meeting 5-27-15==
Who: PJ, EZ, BQ, JE, 2 REU students (Christian and Marquis)

* Explanation of ontologies to new students
* Overview of older AmiGO browser
* Show planteome.cgrb tool for visualizing homology cluster heatmaps and orthology http://planteome.cgrb.oregonstate.edu/heatmap/infoChoice.php
* Used gene set from above to show AgriGO usage

Thursday May 21st, 2015

2015-05-21T15:11:58Z

Elserj: /* B. Update from IT group- Data Store, AmiGO2- Justin Elser */

* Who:
* Not available:

'''Zoom Connection Details: Join from PC, Mac, iOS or Android: https://zoom.us/j/331293888'''

* Link to recording- Video: TBA
* Link to recording- Audio: TBA

== A. General Comments and Updates:==
=== Introductions: ===
Who: GG, PJ,
===Discussion about the Advisory Board===
Suggestions:
* Ruth Bastow

* Sandy Knapp

* From BS: Suggest: Lynn Schriml, just named President of the [http://gensc.org/Genomic Standards Consortium] , (but I am not pressing on her behalf).

== B. Update from IT group- Data Store, AmiGO2- Justin Elser==

===AmiGO 2 progress===

* Working on creating an planteome importer owl file to simplify the loading of the ontologies via the golr Makefile. Working on a catalog xml file to redirect URI in the importer OWL.

* Troubleshooting issue with loading both the environment and trait ontologies where loading both causes the EO to disappear from AmiGO.

===Git migration===
* Trait ontology has been moved to git. Will move the rest after some more testing.

== C. Update from AISO/BisQue group- Justin Preece:==

== D. Update from Ontologies Working Group:==

==E. Other Comments:==

==Next meeting Thursday June 18th, 2015==

Thursday May 21st, 2015

2015-05-21T15:08:30Z

Elserj:

* Who:
* Not available:

'''Zoom Connection Details: Join from PC, Mac, iOS or Android: https://zoom.us/j/331293888'''

* Link to recording- Video: TBA
* Link to recording- Audio: TBA

== A. General Comments and Updates:==
=== Introductions: ===

===Discussion about the Advisory Board===
Suggestions:
* Ruth Bastow

* Sandy Knapp

* From BS: Suggest: Lynn Schriml, just named President of the [http://gensc.org/Genomic Standards Consortium] , (but I am not pressing on her behalf).

== B. Update from IT group- Data Store, AmiGO2- Justin Elser==

===AmiGO 2 progress===

* Working on creating an planteome importer owl file to simplify the loading of the ontologies via the golr Makefile. Working on a catalog xml file to redirect URI in the importer OWL.

* Troubleshooting issue with loading both the environment and trait ontologies where loading both causes the EO to disappear from AmiGO.

== C. Update from AISO/BisQue group- Justin Preece:==

== D. Update from Ontologies Working Group:==

==E. Other Comments:==

==Next meeting Thursday June 18th, 2015==

Thursday May 21st, 2015

2015-05-21T15:08:04Z

Elserj: /* B. Update from IT group- Data Store, AmiGO2- Justin Elser */

* Who:
* Not available:

'''Zoom Connection Details: Join from PC, Mac, iOS or Android: https://zoom.us/j/331293888'''

* Link to recording- Video: TBA
* Link to recording- Audio: TBA

== A. General Comments and Updates:==
=== Introductions: ===

===Discussion about the Advisory Board===
Suggestions:
* Ruth Bastow

* Sandy Knapp

* From BS: Suggest: Lynn Schriml, just named President of the [http://gensc.org/Genomic Standards Consortium] , (but I am not pressing on her behalf).

== B. Update from IT group- Data Store, AmiGO2- Justin Elser==

===AmiGO 2 progress===

Working on creating an planteome importer owl file to simplify the loading of the ontologies via the golr Makefile. Working on a catalog xml file to redirect URI in the importer OWL.

Troubleshooting issue with loading both the environment and trait ontologies where loading both causes the EO to disappear from AmiGO.

== C. Update from AISO/BisQue group- Justin Preece:==

== D. Update from Ontologies Working Group:==

==E. Other Comments:==

==Next meeting Thursday June 18th, 2015==

Thursday May 21st, 2015

2015-05-21T15:07:54Z

Elserj: /* B. Update from IT group- Data Store, AmiGO2- Justin Elser */

* Who:
* Not available:

'''Zoom Connection Details: Join from PC, Mac, iOS or Android: https://zoom.us/j/331293888'''

* Link to recording- Video: TBA
* Link to recording- Audio: TBA

== A. General Comments and Updates:==
=== Introductions: ===

===Discussion about the Advisory Board===
Suggestions:
* Ruth Bastow

* Sandy Knapp

* From BS: Suggest: Lynn Schriml, just named President of the [http://gensc.org/Genomic Standards Consortium] , (but I am not pressing on her behalf).

== B. Update from IT group- Data Store, AmiGO2- Justin Elser==

===AmiGO 2 progress====

Working on creating an planteome importer owl file to simplify the loading of the ontologies via the golr Makefile. Working on a catalog xml file to redirect URI in the importer OWL.

Troubleshooting issue with loading both the environment and trait ontologies where loading both causes the EO to disappear from AmiGO.

== C. Update from AISO/BisQue group- Justin Preece:==

== D. Update from Ontologies Working Group:==

==E. Other Comments:==

==Next meeting Thursday June 18th, 2015==