replaced ZipInputStream in CreateNewDataFilesCommand

[jo-pol]

Why we need this PR:

Zips created by downloading multiple files from an ownCloud service throws java.util.zip.ZipException: only DEFLATED entries can have EXT descriptor when using ZipInputStream to iterate over the entries. This causes the zipfiles to be ingested as is. With ZipFile we don't encounter the exception.

What this PR does:

Replaces ZipInputStream with ZipFile.

• in CreateNewDataFilesCommand
• in ShapefileHandler: abandoned ShapefileHandler constructor with FileInputStream to allow the use of ZipFile

Additional

• for the new iteration method over zip entries in CreateNewDataFilesCommand: extracted methods filteredZipEntries, openZipFile, getShortName and isNotFakeFile
• introduced some unit tests for CreateNewDataFilesCommand or should I call it an integragtion test for the changed classes.
• to allow (or at least simplify) the new unit test, FileUtil.determineFileType catches Bag exceptions The method will now return application/zip rather than throw. Without catching I would need complex mocking to get a BagitFileHandler via CDI just to test the rest.

Which issue(s) this PR closes:

Closes #

Special notes for your reviewer:

Reduce differnces by a compare ignoring white space:
https://github.com/DANS-KNAW/dataverse/pull/199/files?w=1

Suggestions on how to test this:

Upload the zips in src/test/resources/own-cloud-downloads/

• Before deploy: you will get the message Failed to unzip the file. Saving the file as is.
• After deploy: the the zipfiles are split into individuals files, the directory structure is obeyed and sets of shape files are rezipped.

Does this PR introduce a user interface change? If mockups are available, please link/include them here:

no

Is there a release notes update needed for this change?:

Zips downloaded from an ownCloud service are no longer uploaded as is but unzipped.

Additional documentation:
Screenshots of result before and after deploy

[coveralls]

Pull Request Test Coverage Report for Build #81

Details

• 69 of 96 (71.88%) changed or added relevant lines in 4 files are covered.
• 3 unchanged lines in 3 files lost coverage.
• Overall coverage increased (+0.3%) to 20.943%

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Changes Missing Coverage	Covered Lines	Changed/Added Lines	%
src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java	3	6	50.0%
src/main/java/edu/harvard/iq/dataverse/util/ShapefileHandler.java	14	20	70.0%
src/main/java/edu/harvard/iq/dataverse/ingest/IngestServiceShapefileHelper.java	4	12	33.33%
src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateNewDataFilesCommand.java	48	58	82.76%

Files with Coverage Reduction	New Missed Lines	%
src/main/java/edu/harvard/iq/dataverse/util/FileUtil.java	1	38.34%
src/main/java/edu/harvard/iq/dataverse/engine/command/impl/CreateNewDataFilesCommand.java	1	54.58%
src/main/java/edu/harvard/iq/dataverse/util/ShapefileHandler.java	1	67.6%

Totals
Change from base Build #60:	0.3%
Covered Lines:	17492
Relevant Lines:	83522

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💛 - Coveralls