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Rewrite code of CitaviImporter to avoid JAXBContext

Open koppor opened this issue 2 years ago • 18 comments

The code of org.jabref.logic.importer.fileformat.CitaviXmlImporter is written OK, but relies on JAXB. It should be rewritten using StAX-Parser and thus getting rid of a JAXB dependency.

The code reads like we do not hit polymorphism in XMLElements (which is not supported by JAXB. See https://github.com/FasterXML/jackson-modules-base/issues/127).

See https://github.com/JabRef/jabref/blob/d21c11337a17af85047d763218c9df4dbc4db1be/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java#L114 for some code hints.

Similar to https://github.com/JabRef/jabref/pull/9673, the gradle build target generateCitaviSource can be removed and the xsd file be removed from the source repository.

Hints

Example file

  1. Open 7Zip gui
  2. Open src/test/resources/org/jabref/logic/importer/fileformat/CitaviXmlImporterTest4.ctv6bak in 7zip.
  3. Open citavi-single.xml using 7 zip

Initial coding

  1. Remove gradle task generateCitaviSource
  2. Remove src/main/resources/xjc/citavi/citavi.xsd
  3. Exectue gradle clean task.
  4. Observe that CitaviXmlImporter does not compile
  5. Try to understand how MedlineImporter handles XML importing
  6. Work on fixing it. -> You have a) an example file (see above) and b) similar code (MedlineImporter )

Negleted Implementation Option

Thus, it seems to be "just" to include the dependency to jackson module jakarta-xmlbind and to use Jackson's XMLMapper. Code examples are at https://stackify.com/java-xml-jackson/.

koppor avatar Jan 06 '23 14:01 koppor

We should really work on that to get rid off buildSrc

koppor avatar Sep 02 '23 21:09 koppor

Similar code refactoring: https://github.com/JabRef/jabref/pull/9880

koppor avatar Sep 02 '23 21:09 koppor

Hello, I'm a new contributor, and I will carefully read the contribution guidelines. Could you please assign this issue to me? @koppor

JoleneSun111 avatar Oct 11 '23 13:10 JoleneSun111

@JoleneSun111 If you want, you can also try https://github.com/FasterXML/StaxMate. However, that piece of library is not well documented. I would assume that basic Java Stax transformation is enough to solve the issue. - It is not straight-forward, but IMHO manageable nevertheless. The code is backed by tests, so there should be check if everything goes smoothely.

I remember we had the discussions that there have to build local data structures for the lookup of IDs.

koppor avatar Oct 13 '23 11:10 koppor

Hi @koppor, I would like to work on this if this issue is still open?

ShailikaS avatar Dec 28 '23 09:12 ShailikaS

Since there has not been any activity here since the abandoned pull-request from AvunArasi (#9928), I will assign you @ShailikaS.

ThiloteE avatar Dec 28 '23 12:12 ThiloteE

@ShailikaS you have been assigned. Are you still working on this? -- It could be a bit hard to implement...

koppor avatar Jan 22 '24 17:01 koppor

like to take on this issue, if possible

psyren99 avatar Jul 04 '24 22:07 psyren99

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github-actions[bot] avatar Jul 09 '24 22:07 github-actions[bot]