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Core functionality

The core functionality of Bioclipse is provided by a set of managers which are part of the default Bioclipse distribution. This includes the bioclipse, js, ui, and gist managers.

The bioclipse manager

One core manager is the bioclipse manager.

Project and file management

The bioclipse manager has, for example, functionality to convert Eclipse-style paths, based on projects to full operating system-style paths, which you may need in the scripting language. For example, given a project in Bioclipse called WikiPathways with a folder called ``data'', I can get the full path with:

fullPath = bioclipse.fullPath(
  "/WikiPathways/data/" + species + "/"
)

This full path I can then use with, for example, the Java File class from JavaScript and Groovy. For example, I am using Groovy in this set up:

Script code/FullPathWikiPathways.groovy

dataMap = bioclipse.fullPath(
  "/WikiPathways/data/" + species + "/"
);
gpmlFiles = new File(dataMap).listFiles()

Runtime environment

Furthermore, the bioclipse manager has functionality to get some information about the running Bioclipse. You can get the version with:

Script code/BioclipseVersion.groovy

println "Bioclipse " + bioclipse.version()

And get the location of where the log file is found:

bioclipse.logfileLocation()

And provide the locations of a few Bioclipse websites:

bioclipse.wiki()
bioclipse.planet()
bioclipse.bugTracker()

It can be used to test if there is an Internet connection:

Script code/IsOnline.groovy

bioclipse.isOnline()

But it can also fail if Bioclipse does not have active Internet access:

Script code/AssumeOnline.groovy

bioclipse.assumeOnline()

The manager can be used to validate some of these assumptions. For example, it can be used to test which Bioclipse version we are running, or make an assertion on the minimally required version:

bioclipse.requireVersion("2.6.1")

The bioclipse manager is also the place to look if you would like to download a web page, such as the front page of the Dutch newspaper "De Volkskrant":

bioclipse.download("http://www.vk.nl/")

The gist manager

The gist manager is used for downloading gists. A gist is a simple way to share small texts on GitHub, such as Bioclipse scripts and get verson control on them. For more information see https://gist.github.com/ .

Originally, a gist was a single file, but that is past history. The manager followed this change and will now download all files from a gist:

gist.download(6282642)

The js manager

The js manager is one specific for the JavaScript environment. It has a few commands that allow you to interact with the console, for example. To clear the content and write something in the JavaScript console you can use:

js.clear()
js.say("Hello world!")

The ui manager

Another core manager is the ui manager. It has user interface related functionality. For example, we can use it to test if a file is available from the Bioclipse workspace:

knowledgebase = "/WikiPathways/chebi.owl";
if (ui.fileExists(knowledgebase)) {
}

If we combine this with three further commands, we have a means to modify the content of files:

outFilename = "/eNanoMapper/affinity.ttl"
if (ui.fileExists(outFilename)) {
  ui.remove(outFilename)
  ui.newFile(outFilename)
}
ui.append(outFilename, rdf.asTurtle(store))

An Interactive User Interface

Importantly, this manager also takes care of interaction with the Bioclipse user interface itself. For example, we can use it to open editors for particular blobs of data:

ui.open(cdk.fromSMILES("c1=cc=cc=c1"))

And it can show a particular file in the Bioclipse Navigator:

ui.revealAndSelect("/eNanoMapper/affinity.ttl")

The xml manager

There is also an xml manager to work with XML files. For example, we can test if the file is well-formed:

Script code/XMLIsWellFormed.groovy

wellformed = xml.isWellFormed("/Google/solubility.rdf")

And list all the XML namespaces in that file:

Script code/XMLListNamespaces.groovy

wellformed = xml.listNamespaces("/Google/solubility.rdf")

Validation is also possible, using the information in the XML file itself:

Script code/XMLIsValid.groovy

valid = xml.isValid("/Google/solubility.rdf")

This has the disadvantages that this information must be provided and that you likely need internet access. However, you can also validate against a file you provide:

xml.validateAgainstRelaxNG(
  "/Google/solubility.rdf", relaxNGSchemaFile
)
xml.validateAgainstSchematron(
  "/Google/solubility.rdf", schematronFile
)
xml.validateAgainstXMLSchema(
  "/Google/solubility.rdf", xmlSchemaFile
)

The qudt manager

This manager requires Bacting 0.0.30 or higher but allows you to work with quantities:

Script code/UnitConversion.py

quantity = qudt.newQuantity(1.0, "m")
print(quantity)
converted = qudt.convertTo(quantity, "cm");
print(converted)