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Issue 8 #19

Merged
merged 17 commits into from
Mar 22, 2018
Merged

Issue 8 #19

merged 17 commits into from
Mar 22, 2018

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michelole
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This fixes #8.

@michelole
Split parser methods into its own DAO class
934f5f9
@michelole
Move xml tests to proper structure
fa63db7
@michelole
Add xmlunit dependency to test XML files
ab271fb
@michelole
Add method to check existence of the iaa.py script
b9c84ab 
So that it can be used on integration tests on a different package.
@michelole
Fix "unrecognized parameters" bug
1122155 
When two invocations of InterAnnotatorAgreement were made in sequence, the python command would include both previous and current paths, due to the COMMAND variable being static.

This fixes it by creating the full command dynamically.
@michelole
Add example output of iaa.py
784f177
@michelole
Add methods to revert back enums to XML values
d9c16fe
@michelole
Add methods to write a Patient back to XML (fixes bst-mug#8)
ce34df3
@michelole
Add tests for writing a Patient to XML
7ad5d91
@michelole
Add integration tests
9ba94a9 
The tests ensure that XML files generated by PatientDAO can be read and parsed by the iaa.py and generate expected results.
@michelole
DRY Add constants for strings
e343344
@michelole
Change signature of toXML
847d68c 
Receive OutputStream as parameter and do not return null.
@michelole
Move tags creation logic to XMLTag
68dc824
@michelole
Refactor PatientDAO
65a6eb1 
Make methods non-static so that the DocumentBuilder can be reused.
@michelole
Move transformer to a class attribute
2368fcd 
Transformer should be initialized only once. Make it singleton for at least each object creation.
@michelole
Refactor write methods into their own methods
b14e64a
@michelole
Make JDK 8 happy
5a50d5c 
Due to differences between Java 8 and 9 (http://java9.wtf/xml-transformer/), relax the comparison between generated and expected XML files using XMLUnit.

Then, roll back the expected.xml to one closer to the sample files.
@coveralls
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Pull Request Test Coverage Report for Build 17

  • 57 of 72 (79.17%) changed or added relevant lines in 5 files are covered.
  • 1 unchanged line in 1 file lost coverage.
  • Overall coverage increased (+6.6%) to 68.98%
Changes Missing Coverage Covered Lines Changed/Added Lines %
src/main/java/at/medunigraz/imi/bst/n2c2/evaluator/InterAnnotatorAgreement.java 1 8 12.5%
src/main/java/at/medunigraz/imi/bst/n2c2/dao/PatientDAO.java 50 58 86.21%
Files with Coverage Reduction New Missed Lines %
src/main/java/at/medunigraz/imi/bst/n2c2/evaluator/InterAnnotatorAgreement.java 1 13.79%
Totals Coverage Status
Change from base Build 15: 6.6%
Covered Lines: 169
Relevant Lines: 245
💛 - Coveralls

@michelole michelole merged commit 31fe04f into bst-mug:master Mar 22, 2018
@michelole michelole deleted the issue-8 branch March 27, 2018 09:00
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