Navigation
- index
- next |
- previous |
- InterMine documentation »
- Support »
See Release notes for details on each of the InterMine releases.
For non-disruptive releases, you can upgrade your mine by incrementing your version number in your mine’s gradle.properties file:
# example -- flymine's gradle.properties systemProp.imVersion=3.1.1 systemProp.bioVersion=3.1.1
To get patch updates automatically, use the plus (+) notation:
# example -- flymine's gradle.properties systemProp.imVersion=3.1.+ systemProp.bioVersion=3.1.+
Read more about versioning
This is a non-disruptive release.
The class Strain was added to the core InterMine data model in this release.
<!-- core.xml -->
<class name="Strain" extends="BioEntity" is-interface="true">
<attribute name="annotationVersion" type="java.lang.String"/>
<attribute name="assemblyVersion" type="java.lang.String"/>
<collection name="features" referenced-type="SequenceFeature" reverse-reference="strain" />
</class>
<class name="SequenceFeature" extends="BioEntity" is-interface="true">
<!-- snip -->
<reference name="strain" referenced-type="Strain" reverse-reference="features" />
</class>
<class name="Organism" is-interface="true">
<!-- snip -->
<collection name="strains" referenced-type="Strain"/>
</class>
To update to use the new InterMine release:
# example -- flymine's gradle.properties systemProp.imVersion=3.1.+ systemProp.bioVersion=3.1.+
# example -- flymine-bio-sources gradle.properties systemProp.imVersion=3.1.+ systemProp.bioVersion=3.1.+
This release adds Solr to InterMine. To upgrade, you will need to rebuild your database and install Solr.
# example -- flymine's gradle.properties systemProp.imVersion=3.0.+ systemProp.bioVersion=3.0.+
Specifically the postprocesses that build the search index.
You should then be able to deploy your webapp as normal, with the new and improved search.
InterMine 2.0 is a disruptive release and is not backwards compatible. This means that databases, webapps and code from previous releases will need to be updated to work with the new InterMine release. Below are detailed instructions on how to migrate your InterMine to the new build system.
Warning
If you have custom InterMine code, your changes will likely not work as expected after the upgrade. Please contact us and we can help you migrate your edits to the new system.
Please contact us if you have any questions or concerns! We have a mailing list or you can contact us directly via email or our discord channel (chat.intermine.org). If you are having difficulties, we can also arrange a skype call to walk through any problems together. Please make sure your code is public, e.g. GitHub, so we can help test!
InterMine now uses Gradle to manage dependencies and to build and run InterMine. Please see Gradle Quick Start for useful Gradle commands and Gradle FAQs for help with common questions and errors.
See the Gradle blog post for details as to why we made this change.
You will need Maven installed. We use Maven to manage mine-specific InterMine dependencies, including your mine-specific data parsers.
# for Ubuntu
sudo apt-get install maven
You do not need to install Gradle locally. Instead, use the Gradle wrapper provided.
Previously you had to download and compile InterMine. Now, instead, you’ll be using the compiled InterMine JARs available via Maven. This means you should remove all InterMine code from your mine repositories. Your mine repositories should only contain your mine (webapp and dbmodel) and your mine’s custom data sources.
If you have your mine and bio/sources in your InterMine checkout, instead of in their own repository, you’ll have to separate them out.
What you want to end up with:
- FlyMine - https://github.com/intermine/flymine/ (MUST be the name of your mine)
- FlyMine specific data sources - https://github.com/intermine/flymine-bio-sources
Options to separate out your mine repo:
# don't do this
~/git $ cp intermine/flymine flymine; cd flymine
~/git/flymine $ git init; git add *; git commit -am "initial commit"
You should not have any core InterMine code locally.
InterMine has switched to use the standard Maven directory structure.
src/main/java
src/main/resources
src/test/java
src/test/resources
You will have to run two migration scripts to move your current mine over to this new layout – one script for your mine and one for your mine’s data parsers. The migration scripts are located in the intermine-scripts repository.
~/git $ git clone https://github.com/intermine/intermine-scripts.git
Run “migrateMine” script to move your mine over to the new directory system. You might want to create a new gradle branch for testing.
~/git/intermine-scripts/gradle-migration/mine $ ./migrateMine.sh ~/git/flymine
Run the “migrateBioSources” script to move your sources over to the new directory system.
~/git/intermine-scripts/gradle-migration/data-sources $ ./migrateBioSources.sh ~/git/flymine-bio-sources
Run this command to put your sources on the classpath and therefore available to the database build:
# not part of the upgradle process. You will install every time you make a change
~/git/flymine-bio-sources $ ./gradlew install --stacktrace
This task builds the JARs and places them on your classpath in ~/.m2/repository.
Note the command is ./gradlew instead of gradle. Use the provided Gradle wrapper instead of locally installed Gradle.
You will have to install your sources every time you update the source code to update the JAR being used by the build.
Previously the data model was merged from all data sources’ additions XML file. This is no longer true. Since each source is in its own JAR now, the data model is self-contained. Therefore if you reference a class in your data parser, it must be present in the additions file. Alternatively, you can specify a single data model file that will be merged into each source:
// [in build.gradle in root of your mine bio/sources directory, e.g. flymine-bio-sources]
// uncomment to specify an extra additions file for your bio-sources
// this file will be merged with the additions file for each data source
// and included in each source JAR.
//bioSourceDBModelConfig {
// # file should live in your mine's bio/sources directory
// globalAdditionsFile = "MY-MINE_additions.xml"
//}
Please see Gradle Quick Start for details on Gradle and common Gradle commands and Gradle FAQs for help with common questions and errors.
See the Model Changes blog post for details.
You have may to update your data sources and queries to match the new data model.
Software dependency requirements have been updated to the latest versions. This is so we can get rid of legacy code and make use of new features.
Java SDK 8
Tomcat 8.5.x
Postgres 9.3+
You will get errors if you use older versions. e.g. If you use Java 7, you will get this error: Caused by: java.security.NoSuchProviderException: no such provider: SunEC
We are making some non-backwards compatible changes to our API. These three end points have a parameter called xml which holds the XML query. We are going to rename this parameter to be query (as we now accept JSON queries!) to match the syntax of all the other end points.
/query/upload
/template/upload
/user/queries (POST)
Please update any code that references these end points.
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 /git/index for details.
If you host a copy of the CDN, then you should also pull in changes from that repository.
The core model of InterMine has changed in release 1.1 so you may encounter more errors than usual.
| 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 |
| class | old | new |
|---|---|---|
| ProteinDomain | proteins | proteinDomainRegions |
| Protein | proteinDomains | proteinDomainRegions |
| ProteinDomainRegion | – | start |
| – | end | |
| – | identifier | |
| – | database |
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 /get-started/hikaricp 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>
This code will work with any webapp and database created with InterMine 1.3+.
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.
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.
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.
The core model of InterMine has changed in release 1.1 so you may encounter more errors than usual.
Updated to latest version of Sequence Ontology, 2.5
| old | new |
|---|---|
| Comment.text | Comment.description |
| Gene.ncbiGeneNumber | – |
| – | Gene.description |
| – | Gene.briefDescription |
| class | old | new |
|---|---|---|
| Interaction | gene | gene1 |
| interactingGenes | gene2 | |
| type | details.type | |
| role | details.role1 | |
| – | details.role2 | |
| name | details.name | |
| shortName | – | |
| InteractionRegion | primaryIdentifier | – |
| name | – |
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:
# in ~/.intermine/MINE_NAME.properties
resolver.entrez.file=/DATA_DIR/ncbi/gene_info
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