Rewrite code of CitaviImporter to avoid JAXBContext

[koppor]

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 FasterXML/jackson-modules-base#127).

See

jabref/src/main/java/org/jabref/logic/importer/fileformat/MedlineImporter.java

Line 114 in d21c113

while (reader.hasNext()) {

for some code hints.

Similar to #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]

We should really work on that to get rid off buildSrc

[koppor]

Similar code refactoring: #9880

[JoleneSun111]

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

[koppor]

@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.

[ShailikaS]

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

[ThiloteE]

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

[koppor]

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

[psyren99]

like to take on this issue, if possible

[koppor]

Seems to be too hard for programming newcomers, therefore removed from "good first issues".

[koppor]

/assign @psyren99

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