Increase checksum noting and matching for imports. (rebase)

[mtbc]

To test make sure that different import/upload paths still work, including attaching files as annotations. For real files in the server's local filesystem, if they have a corresponding entry in the originalfile table in the DB then make sure that the SHA1 there is set correctly.

The rebase of #890 clashed poorly with refactoring on develop. In ManagedImportProcessI.java mostly it just adjusts the style of the code to more closely fit what is on dev_4_4.

[joshmoore]

Importing and attaching checksums look correct:

omero=# select id, repo, path, name, sha1, size from originalfile order by id desc limit 10;
 id  |                 repo                 |                           path                            |        name         |                   sha1                   |   size
-----+--------------------------------------+-----------------------------------------------------------+---------------------+------------------------------------------+----------
 348 |                                      | /Users/moore/NoBackup/SampleImages/                       | a.fake              | 55ca6286e3e4f4fba5d0448333fa99fc5a404a73 |        3
 347 | 149719c7-c467-4f8d-9d25-0e3d751e69fa | user-6_7/2013-03/26/4293122335/                           | a.fake              | 55ca6286e3e4f4fba5d0448333fa99fc5a404a73 |        3
 ...
 345 | 149719c7-c467-4f8d-9d25-0e3d751e69fa | user-6_7/2013-03/26/4293025734/                           | a.fake              | 55ca6286e3e4f4fba5d0448333fa99fc5a404a73 |        3

[joshmoore]

Same fake checksum test as 890 - 👍

omero@gretzky:~/OMERO-CURRENT/pr947$ JAVA_OPTS="-cp .:$CLASSPATH" ../bin/omero -w ome -s user-6@localhost import ../*.fake
...
2013-03-26 10:39:35,518 4371       [      main] INFO   ormats.importer.cli.LoggingImportMonitor  - FILESET_UPLOAD_START
FAKE CHECKSUM
2013-03-26 10:39:35,545 4398       [      main] INFO   ormats.importer.cli.LoggingImportMonitor  - FILE_UPLOAD_STARTED: /home/omero/slave/workspace/OMERO-merge-develop/src/dist/pr947/../pr947.fake
2013-03-26 10:39:35,712 4565       [      main] INFO   ormats.importer.cli.LoggingImportMonitor  - FILE_UPLOAD_COMPLETE: /home/omero/slave/workspace/OMERO-merge-develop/src/dist/pr947/../pr947.fake
2013-03-26 10:39:35,730 4583       [      main] INFO   ormats.importer.cli.LoggingImportMonitor  - FILESET_UPLOAD_END
2013-03-26 10:39:35,734 4587       [      main] ERROR        ome.formats.importer.ImportLibrary  - Error on import
omero.ValidationException
    serverStackTrace = ""
    serverExceptionClass = ""
    message = "file checksum mismatch on upload: user-6_7/2013-03/26/4294375152/pr947.fake (client has fake, server has ea75706155cffed0a1bd43ddba4543da27d73a67)"
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
        at java.lang.Class.newInstance0(Class.java:355)
        at java.lang.Class.newInstance(Class.java:308)
        at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2243)
        at IceInternal.BasicStream.throwException(BasicStream.java:1632)
        at IceInternal.Outgoing.throwUserException(Outgoing.java:442)
        at omero.grid._ImportProcessDelM.verifyUpload(_ImportProcessDelM.java:352)
        at omero.grid.ImportProcessPrxHelper.verifyUpload(ImportProcessPrxHelper.java:458)
        at omero.grid.ImportProcessPrxHelper.verifyUpload(ImportProcessPrxHelper.java:430)
        at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:397)
        at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:169)
        at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:143)
        at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:479)
2013-03-26 10:39:35,747 4600       [      main] INFO         ome.formats.importer.ImportLibrary  - Exiting on error