Commits

Author Commit Message Labels Comments Date
Raza Ali
Test for Concurrent Access to Model storage added New test checks whether two threads beginning at the same time can access VcsManager concurrently if they are accessing different models. This is done by having one read a small model, and another write a large one, and asserting whether the former terminates before the latter. The reliability of the test is increased as the file size for the second thread is increased. However, the execution time…
Raza Ali
Quickfix to Concurrency tests
Raza Ali
Partial implementation of concurrency testing
Raza Ali
GitManager syncrhonised at model level Previous implementation did not allow concurrent access to the repository. This has been modified to be at model-level. Tests pass currently but are single-threaded. Concurrency testing needs to be performed!
Mihai Glonț
Draft BatchImport script as a potential means of submitting models to JUMMP. For the time being, BatchImport only takes care of the prerequisites of the submission, without actually submitting the models. This will be added later. Refer to the script's documentation for usage details. Also added a note in TestCore to say that it is no longer of use.
Mihai Glonț
Added integration tests that simulate the submission workflow. The new tests can be used to populate Jummp with a selection of models contained within a predefined folder. Warning: the database is dropped after the test finishes if the testing environment is used.
Mihai Glonț
Configured Hibernate to release database connections. As a result, we now no longer see ERROR util.JDBCExceptionReporter - Cannot get a connection, general error in the logs. Hopefully it stays that way for good.
Mihai Glonț
Created replacement for the jummp loader. Jummp-loader requires updating to reflect the latest changes to the model storage infrastructure. In the meanwhile, we have developed a sequence of tests that cover the same functionality.
Mihai Glonț
Do not fetch publication details from using CiteXplore. Temporarily keep publication = null until we use EuropePMC web services.
Mihai Glonț
Updated integration tests to use FileSystemService where appropriate. This also means that we ensure that no test models are created in the root model directory.
Raza Ali
SbmlService tests modified to have one model file per directory Current implementation of SbmlService returns the first file in the model directory that is a valid Sbml document. This is problematic for cases where multiple model files are in the directory. We need a non-arbitrary way of getting to the model file we want, instead of getting the first one (or most recent, etc). For now the tests are written to have one model file per directory.
Mihai Glonț
Updated ModelServiceTests to use the FileSystemService.
Mihai Glonț
Merge branch 'master' of https://bitbucket.org/MihaiGlont/jummp
Mihai Glonț
Temporarily disable forked execution due to Grails' logging conflicts. When we run grails using grails.project.fork.run=true we get a NoClassDefFoundError caused by org/apache/commons/beanutils/BeanUtils which is needed by log4j.
Raza Ali
Tests pass, but by disabling caching in SbmlService. Good and bad. Need to investigate further.
Raza Ali
Tests passed, SbmlService tests and Bives issues fixed GitManager writes to a temporary directory (within exchange) for each retrieve call. Revision events are generated with retrieved files from revisions instead of passing the original files around (which were being read by Revision Created Listener resulting in on-and-off SbmlService test failure). Revision Created Listener has the responsibility of deleting the temp files created for Revision Cre…
Raza Ali
ModelService Integration tests passed Integration tests passed for model service. However they required disabling of Bives revision created listener as it was retrieving the same files from VCS as were being tested. Current implementation does not use a different name for each retrieve call resulting in tests failing for when the same named file of different revisions was retrieved by clients of the vcs API. The simple fix is to creat…
Mihai Glonț
Merge branch 'master' of https://bitbucket.org/MihaiGlont/jummp
Raza Ali
Fix to GitManager to use current directory only for repository Previous implementation of GitManager used to scan up the file directory to find the repository. This no longer works, as the repository must be in the directory provided to GitManager.
Mihai Glonț
Merge branch 'master' of https://bitbucket.org/MihaiGlont/jummp
Raza Ali
Added back working directory config parameter to tests I had mistakenly removed the parameter from tests as its no longer used by VcsManager without realising it is now used by the filesystem service.
Mihai Glonț
Cleaned up the output of the debug log. We are no longer interested in the behaviour of the URL mapping, nor in that of the Quartz scheduler. We are merely tracing our own classes.
Raza Ali
Tests for ModelService partially passed UploadModel tests of ModelService passed, requiring changes to ModelService and SbmlService.
Mihai Glonț
Run Tomcat in forked execution mode. It decreases memory consumption due to the fact that the Grails build system can exit after it finishes, so the JVM can reclaim that memory.
Mihai Glonț
Updated ModelServiceTests to accommodate changes in method signature. ModelService.retrieveModelFiles now returns a map of file names and corresponding byte arrays, rather than a single byte array, since there might be multiple files belonging to that model. The tests now reflect this change.
Raza Ali
Bug fix in RemoteModelAdapterDBusImpl
Raza Ali
Merge branch 'master' of https://bitbucket.org/MihaiGlont/jummp
Raza Ali
Changes to DBus/Remote classes for retrieveModel functions.
Mihai Glonț
Merge branch 'master' of https://bitbucket.org/MihaiGlont/jummp
Mihai Glonț
Refactored RevisionCreatedListener to cope with multiple files. Bives can now handle the list of files that are associated with a Revision. We need to decide how to handle the diff if a model is split over multiple files. Fixed a minor bug in ModelService and some formatting issues in SbmlService for added consistency.
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