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See merge request uniprot-public/unifire!26

2021.4

See merge request uniprot-public/unifire!25

# Conflicts:
#   procedures/src/main/java/uk/ac/ebi/uniprot/urml/procedures/unirule/positionalfeatures/PositionalMapper.java

Simplifies merging of FactSets in UniFireRunner

Improved comment

- Close XMLStreamReader throughPartialUnmarshaller and FactSetChunkParser

- Updated logging

- Updated logging

- Aggregate and merge FactSets when read protein-by-protein

- FactSetChunkParser parsing strategy does not apply to URML-XML

- Disabled Access Warnings for PIRSRApp
- Removed InterProXmlProteinChunkParser.java

- Unified FactSetChunkParsers for InterPro-XML, URML-XML and UniParc-XML
- Use ChunkParsers instead of Partitioner to split Fact data in UniFireRunner. This will limit the amount of Heap space for large protein input data

Improved logging

- Call completeWrite when closing URMLFactWriter
- Set isValid and idMapped properties in PositionalMapper
- Removed duplicated testcase

Committed InterProScan output for tests

- Plugged InterProXmlProteinChunkParser into PIRSRRunner
- Added test for InterProXmlProteinChunkParser

- Added InterProXmlProteinChunkParser using new PartialUnmarshaller.java and plugged it into PIRSRRunner

TRM-26114:

Closes TRM-26114

See merge request uniprot-public/unifire!23

- Reorganised hierarchy of io xml packages
- Added PartialUnmarshaller and InterProProteinChunkParser

- Silenced java illegal reflective access warning for jaxb
- Log feature size not kept at debug in stead of warning level

2021.3

See merge request uniprot-public/unifire!22

TRM-24657 & TRM-25489 Migration to java11

Closes TRM-24657

See merge request uniprot-public/unifire!12

Older version of 3.7 was not able to resolve ClassUtils.isAssignable(javaType, Number.class) and causing NullPointerException

2021.2

See merge request uniprot-public/unifire!21

Log exceptions

See merge request uniprot-public/unifire!19

Made InterProXmlToFactConverter usable as a stand-alone tool Application

Set default version of the container image to 2021.1.1

See merge request uniprot-public/unifire!18

TRM-24976 Disable PIRSRAppIntegrationTest

Closes TRM-24976

See merge request uniprot-public/unifire!17

Manage resource with try-with-resources

See merge request uniprot-public/unifire!16

Removed unused field