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• Release Notes v1.22
• Implemented checks:
  • IDF Checks
  • SDRF Checks
• Downloads

Command Line Usage

Download the latest jar and run:

java -jar magetabcheck-jar-with-dependencies.jar /path/or/url/to/idf

where /path/or/url/to/idf could be a local path to idf file or an URL.

Additional Java options:

• -Defo.cachedir=/efo/cache/dir - to cache EFO locally and prevent downloading it with every run
• -Dchecker.debug=true - to turn debug output on/off

E.g.

java -Dchecker.debug=true -jar magetabcheck-jar-with-dependencies.jar \
     http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-868/E-MTAB-868.idf.txt

java -Defo.cachedir=/tmp/efo-cache -jar magetabcheck-jar-with-dependencies.jar \
     /Users/bob/my-experiments/E-MTAB-123/E-MTAB-123.idf.txt

Maven dependency

<dependency>
   <groupId>uk.ac.ebi.fg.annotare2</groupId>
   <artifactId>magetabcheck</artifactId>
   <version>1.21</version>
</dependency>

E.g. Running checks on IDF-SDRF pair stored somewhere locally:

final LimpopoBasedChecker checker = new LimpopoBasedChecker();
...
Collection<CheckResult> results = checker.check("/path/to/your/IDF");

E.g. Running checks on IDF-SDRF pair created on a fly:

final LimpopoBasedChecker checker = new LimpopoBasedChecker();
...
MAGETABInvestigation investigation = new MAGETABInvestigation();
investigation.IDF = // create IDF  
investigation.SDRF = // create SDRF
Collection<CheckResult> results = checker.check(investigation);

E.g. Specifying Guice module:

final LimpopoBasedChecker checker = new LimpopoBasedChecker(yourGuiceModule);
...

E.g. Overriding MageTabCheck module:

Injector injector = Guice.createInjector(Stage.DEVELOPMENT,
                override(new CheckerModule()).with(new YourGuiceModule()));
...
@Inject
MageTabChecker checker;
...
Collection<CheckResult> results = checker.check(experiment); 

Note: EFO service initialization takes time, especially if it is not cached during previous runs and has to be downloaded. If you are planning to run the checker more than once I'd suggest to create a single instance of checker and use it as a service. To prevent EFO file download with every application start set -Defo.cachedir=.. property.

Properties

(since v1.5)

An alternative way to specify the checker properties is a property file, e.g.:

checker.debug = false
efo.url = http://www.ebi.ac.uk/efo/efo.owl
efo.cachedir = /efo/cache/dir
owlapi.entityExpansionLimit = 200000

You can put it into the classpath of your application (named MageTabCheck.properties) or specify the path as VM option in command line:

java -Dchecker.properties=/path/to/my-checker.properties -jar magetabcheck-jar-with-dependencies.jar \
     http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-868/E-MTAB-868.idf.txt

Key	Details	Default
checker.debug	Shows debug output if true	true
efo.url	Experimental Factor Ontology URL	http://www.ebi.ac.uk/efo/efo.owl
efo.cachedir	Experimental Factor Ontology cache dir	Not cached
owlapi.entityExpansionLimit	An OWL API setting to tune EFO parse	200000

Note: A property value specified as -D<property-key>=... has the highest priority, so it overrides the value set in property file.