Convert Combine Archive (OMEX) to/from Research Object Bundle.
(c) University of Manchester 2014 http://www.mygrid.org.uk/
License: MIT License
This tool enrich/convert OMEX Combine Archives so that they are also valid RO Bundles.
This is achieved by parsing the OMEX manifest and creating the equivalent RO Bundle manifest (or vice versa), using the RO Bundle API.
Note that the actual implementation for parsing and generating the OMEX manifest is now a standard part of the RO Bundle API. For details, see the Java package org.purl.wf4ever.robundle.manifest.combine
OMEX Combine Archives have similar mechanism of describing the bundled resources in a manifest.
An OMEX archive can also be a valid RO Bundle, and an RO Bundle can also be an OMEX archive, simply by having both manifests included in the ZIP archive. (as long as you don't then modify the archive without updating both manifests!)
The conversion therefore parses the OMEX manifest
using an
XSD Schema,
and creates equivalent entries in the RO Bundle manifest, copying over the
format information to either
mediatype or conformsTo (depending if it is an absolute URI).
When parsing the OMEX manifest.xml, location is interpreted as an
unescaped path within the bundle (relative to the manifest.xml)
Absolute URIs in location are supported, recorded as an uri aggregation in
the RO bundle.
The base URI for files in the archive
is generated using the app:// URI scheme
according to the RO bundle specifications for absolute
URIs. So
this means URIs in files are parsed with a base URI like:
app://5226267e-75b1-48c4-b9da-ea587023adda/manifest.xml - thus
also allowing for slash-based URI references like / and /metadata.rdf.
In OMEX, metadata is always given in metadata.* files. We'll parse
metadata.rdf, and look for any subjects that are aggregated
by the archive (or is the archive itself), and then add metadata.rdf to
annotations in the RO bundle manifest for each described file.
(TODO: Support additional metadata files)
The metadata file is also examined for dcterms:created, dcterms:modified
and dcterms:modified annotations, which are propagated into the RO Bundle
manifest. The timestamp of affected files in the ZIP archive will also be set
to the specified modified time from this metadata, if it exists.
Note that the RO Bundle mimetype
file is not added, as an OMEX archive (and its
specialization) can be viewed as a more application-specific specialization of
RO Bundles, as allowed for in the RO bundle container
specification. OMEX archives
however do not currently have such a specific mimetype, just an extension varying
with the application type (e.g. .sbex for SBML archive).
Prerequisites:
To build, simply do mvn clean install:
stain@biggie:~/src/ro-combine-archive$ mvn clean install
[INFO] Scanning for projects...
[INFO]
[INFO] ------------------------------------------------------------------------
[INFO] Building Combine Archive / RO interoperability 0.1.0-SNAPSHOT
[INFO] ------------------------------------------------------------------------
...
[INFO] --- maven-install-plugin:2.4:install (default-install) @ ro-combine-archive ---
[INFO] Installing /home/stain/src/ro-combine-archive/target/ro-combine-archive-0.1.0-SNAPSHOT.jar to /home/stain/.m2/repository/org/researchobject/ro-combine-archive/ro-combine-archive/0.1.0-SNAPSHOT/ro-combine-archive-0.1.0-SNAPSHOT.jar
[INFO] Installing /home/stain/src/ro-combine-archive/pom.xml to /home/stain/.m2/repository/org/researchobject/ro-combine-archive/ro-combine-archive/0.1.0-SNAPSHOT/ro-combine-archive-0.1.0-SNAPSHOT.pom
[INFO] Installing /home/stain/src/ro-combine-archive/target/ro-combine-archive-0.1.0-SNAPSHOT-sources.jar to /home/stain/.m2/repository/org/researchobject/ro-combine-archive/ro-combine-archive/0.1.0-SNAPSHOT/ro-combine-archive-0.1.0-SNAPSHOT-sources.jar
[INFO] Installing /home/stain/src/ro-combine-archive/target/ro-combine-archive-0.1.0-SNAPSHOT-test-sources.jar to /home/stain/.m2/repository/org/researchobject/ro-combine-archive/ro-combine-archive/0.1.0-SNAPSHOT/ro-combine-archive-0.1.0-SNAPSHOT-test-sources.jar
[INFO] Installing /home/stain/src/ro-combine-archive/target/ro-combine-archive-0.1.0-SNAPSHOT-tests.jar to /home/stain/.m2/repository/org/researchobject/ro-combine-archive/ro-combine-archive/0.1.0-SNAPSHOT/ro-combine-archive-0.1.0-SNAPSHOT-tests.jar
[INFO] Installing /home/stain/src/ro-combine-archive/target/ro-combine-archive-0.1.0-SNAPSHOT-standalone.jar to /home/stain/.m2/repository/org/researchobject/ro-combine-archive/ro-combine-archive/0.1.0-SNAPSHOT/ro-combine-archive-0.1.0-SNAPSHOT-standalone.jar
[INFO] ------------------------------------------------------------------------
[INFO] BUILD SUCCESS
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 45.570s
[INFO] Finished at: Fri Apr 25 19:51:41 BST 2014
[INFO] Final Memory: 41M/303M
[INFO] ------------------------------------------------------------------------
Alternatively you can download the ro-combine-archive 0.1.0 standalone.
Note that this download might not reflect the latest features as when building from source.
To execute from the self-contained JAR, try:
java -jar target/ro-combine-archive-0.1.0-SNAPSHOT-standalone.jar [omex-file ...]
Note that the given OMEX Combine Archive will be updated in-place to also
include .ro/manifest.json, making it an RO bundle.
This examples copies the example Boris.omex file to target (because we'll change it), then
executes the ro-combine-archive converter:
stain@biggie:~/src/ro-combine-archive$ cp src/test/resources/Boris.omex target
stain@biggie:~/src/ro-combine-archive$ java -jar target/ro-combine-archive-0.1.0-SNAPSHOT-standalone.jar target/Boris.omex
log4j:WARN No appenders could be found for logger (org.apache.jena.riot.stream.JenaIOEnvironment).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Apr 25, 2014 7:56:26 PM org.purl.wf4ever.robundle.utils.RDFUtils literalAsFileTime
INFO: Literal not an XSDDateTime, but: class java.lang.String 2013-05-28T17:50:43.999+01:00
Inspecting the modified archive will reveal the added .ro/manifest.json:
stain@biggie:~/src/ro-combine-archive$ cd target/
stain@biggie:~/src/ro-combine-archive/target$ unzip Boris.omex
Archive: Boris.omex
inflating: BorisEJB.xml
inflating: manifest.xml
inflating: metadata.rdf
creating: paper/
inflating: paper/Kholodenko2000.pdf
creating: .ro/
inflating: .ro/manifest.json
Inspecting .ro/manifest.json:
{
"@context" : [ "https://w3id.org/bundle/context" ],
"id" : "/",
"manifest" : [ "/.ro/manifest.json", "/manifest.xml" ],
"createdOn" : "2013-05-28T16:50:43.999Z",
"aggregates" : [ {
"file" : "/paper/Kholodenko2000.pdf",
"folder" : "/paper/",
"mediatype" : "application/pdf",
"createdOn" : "2013-04-05T08:16:08Z",
"proxy" : "urn:uuid:ca91dfa3-729b-4494-a059-b73b9b3c4261"
}, {
"file" : "/metadata.rdf",
"folder" : "/",
"createdOn" : "2014-04-25T18:17:00Z",
"conformsTo" : "http://identifiers.org/combine.specifications/omex-metadata",
"proxy" : "urn:uuid:850812ed-88d5-4999-9675-8257355f6e3e"
}, {
"file" : "/BorisEJB.xml",
"folder" : "/",
"createdOn" : "2012-10-29T10:58:38Z",
"conformsTo" : "http://identifiers.org/combine.specifications/sbml",
"proxy" : "urn:uuid:054c9840-0283-4a3c-8319-b0e24b6593b4"
}, {
"uri" : "http://www.ebi.ac.uk/biomodels-main/BIOMD0000000010",
"conformsTo" : "http://identifiers.org/combine.specifications/sbml"
} ],
"annotations" : [ {
"about" : "/",
"content" : "/metadata.rdf"
} ]
}