Upgrade Instructions

To pull changes in your local repository and merge them into your working files:

$ git pull upstream

If you don’t have a git repo yet, see Get the Software for details.

If you host a copy of the CDN, then you should also pull in changes from that repository.

Upgrade to InterMine 1.6

The core model of InterMine has changed in release 1.1 so you may encounter more errors than usual.

update integration keys

You may need to update your integration keys if they are using a class or field that’s been changed.

update custom converter

If you are storing data using a class or field that’s been changed, you will have to change your code to use the new model. See below for the complete list of model changes.

template queries

You will have to update your templates to use the new model

interaction viewer

The cytoscape tool uses the new model - will not work until you build a database with the new code

Interactions

class	old	new
Interaction	gene1	participant1
	gene2	participant2
	relationshipType (Term)	relationshipType (String)
InteractionDetail	allInteractors (Gene)	allInteractors (Interactor)
Interactor	–	stoichiometry
	InteractionDetail.role1	role
	InteractionDetail.type	type

Protein Domains

class	old	new
ProteinDomain	proteins	proteinDomainRegions
Protein	proteinDomains	proteinDomainRegions
ProteinDomainRegion	–	start
	–	end
	–	identifier
	–	database

Upgrade to InterMine 1.4

There are no model changes, but we’ve added some new features that require an update.

We’ve added a new fancy connection pool, you should see a performance improvement. However you do need to update some configuration files.

The number of database connections required will depend on your usage. 100 connections is the default and should be okay for production webapps. However each webapp reserves 20 connections so on your dev machines it may be wise to raise the maximum quite a bit.

postgresql.conf

max_connections=250

in your $MINE directory:

default.intermine.integrate.properties

set

db.production.datasource.maxConnections=20

db.common-tgt-items.datasource.maxConnections=5

and for each database replace

db.production.datasource.class=org.postgresql.ds.PGPoolingDataSource

(or any other db pooling class)

with these 2 lines

db.production.datasource.class=com.zaxxer.hikari.HikariDataSource db.production.datasource.dataSourceClassName=org.postgresql.ds.PGSimpleDataSource

default.intermine.webapp.properties

set

db.production.datasource.maxConnections=20

and for each database replace

db.production.datasource.class=org.postgresql.ds.PGPoolingDataSource

(or any other db pooling class)

with these 2 lines

db.production.datasource.class=com.zaxxer.hikari.HikariDataSource db.production.datasource.dataSourceClassName=org.postgresql.ds.PGSimpleDataSource

Any other data source you use should be set to five connections, raised to ten if you encounter problems, e.g. the build failing with an error like so:

Error message

Caused by: org.postgresql.util.PSQLException: FATAL: connection limit exceeded for non-superusers

Or this (See #912)

Error message

Unable to get sub-ObjectStore for Translating ObjectStore

See HikariCP and InterMine settings for details.

The metadata package has moved from to InterMine-model. If you have custom data sources that use InterMine Utils, you may have to update your code to reflect the new location. Your IDE should be able to do this for you.

Add clearReferencesStopTimerThreads to your $TOMCAT/conf/context.xml file, so it should look like so:

<Context sessionCookiePath="/" useHttpOnly="false" clearReferencesStopTimerThreads="true">
...
</Context>

Upgrade to InterMine 1.3.x

This code will work with any webapp and database created with InterMine 1.3+.

Upgrade to InterMine 1.3

• Remove all duplicate entries from web.xml
• Model changes:
  • DataSet now has a publication reference
  • AnnotationExtension has been moved from GOAnnotation to GOEvidence.

Also, we have changed our GO parser a bit. Each line in a gene annotation file now corresponds with an Evidence object. In prior releases, each Evidence object was unique, e.g. only a single evidence code per gene / GO term pair.

Upgrade to InterMine 1.2.1

If you have your own home page (begin.jsp), you must manually make this change: 501e221

This is a fix for the keyword search - when users submit a blank search form, see Issue #329

There are no model or configuration changes in this release.

Upgrade to InterMine 1.2

The core data model has not been changed, so you should be able to release a webapp using InterMine 1.2 code without making any changes.

Upgrade to InterMine 1.1

The core model of InterMine has changed in release 1.1 so you may encounter more errors than usual.

update integration keys

You may need to update your integration keys if they are using a class or field that’s been changed.

update custom converter

If you are storing data using a class or field that’s been changed, you will have to change your code to use the new model. See below for the complete list of model changes.

template queries

You will have to update your templates to use the new model

interaction viewer

Widget uses the new model - will not work until you build a database with the new code

Updated to latest version of Sequence Ontology, 2.5

old	new
Comment.text	Comment.description
Gene.ncbiGeneNumber	–
–	Gene.description
–	Gene.briefDescription

Interactions

class	old	new
Interaction	gene	gene1
	interactingGenes	gene2
	type	details.type
	role	details.role1
	–	details.role2
	name	details.name
	shortName	–
InteractionRegion	primaryIdentifier	–
	name	–

Gene Ontology

class	old	new
GOAnnotation	withText	evidence.withText
	with	evidence.with
	–	annotationExtension
OntologyTerm	–	crossReferences [1]

[1]	used for Uberon

Identifiers

We have several [wiki:Homologue new homologue data converters] available in this InterMine release. However, some of these new data sources use Ensembl IDs. If you want to load the model organism database identifier instead (important for interoperation with other InterMines), you should use the Entrez Gene ID resolver:

1. Download the identifier file - ftp://ftp.ncbi.nih.gov/gene/DATA/gene_info.gz
2. Unzip the file
3. Add the path to properties file:

# in ~/.intermine/MINE_NAME.properties
resolver.entrez.file=/DATA_DIR/ncbi/gene_info

Configuration Updates

Web services uses the webapp.baseurl property to run queries, so be sure this is the valid URL for your mine. Otherwise you will get an “Unable to construct query” error on the query results page.

# in ~/.intermine/MINE_NAME.properties
# used by web services for running queries, needs to be valid
webapp.baseurl=http://localhost:8080