Directory 'trunk' created by IntelliJ IDEA
Initial commit of dbxpModuleStorage. Reads tab delimited file and stores in MongoDB (see DataMatrixTests.groovy)
removed Assay/Sample/Study; mongo and hibernate play nicely together now, added uploadedFileName property to DataMatrix (also set some initial values correctly by default now); strings are not interpreted anymore; added some querying tests
started implementing changes from task list on google doc; using ParsedFile + UploadedFile instead of DataMatrix
Default to failOnError: true for saves
Using matrixImporter for file reading
Fixed some nullable issues with domain classes
created UploadedFileService
updated tests
Now using current matrix importer
added smaller test data set
Changed package name from pocModule to dbxpModuleStorage
added assay property to UploadedFile and uploader of type org.dbxp.moduleBase.User
- Rudimentary file upload handler in ParsedFileController
- extended Assay to work with UploadedFile (AssayWithUploadedFile)
- added methods for data retrieval from parsed files in ParsedFileService
- added some dependencies in order for the plugin to be able to run independently with inplace plugins (should not be necessary later when using proper plugins)
- moved uploadFinished action to UploadedFileController
- added (untested) rest controller
- added AssayService with some logic for rest controller
- added UploadedFileService.getUploadedFilesForUser which now simply returns all uploaded files (will change)
Uploading a file now gets saved as UploadedFile (if less than 4MB!)
- Renamed assayService to assayWithUploadedFileService to better distinguish it from the AssayService from dbxpModuleBase
- renamed getMeasurementNames to getFeatureNames
- UploadedFile now uses GridFS to be able to store large files
- also added UploadedFile.parse convenience method; also links newly created parsed file to uploaded file (old way still possible)
- added getFilesUploadedByUser, getUploadedFilesFromAssaysReadableByUser and implemented getUploadedFilesForUser
- storing fileSize and fileName in UploadedFile as well instead of just in the GridFSFile
Temporary workaround for issues with services in domain object when using mongo
- added setUploadedFile convenience method to AssayWithUploadedFile
- added isColumnOriented property to ParsedFile
- changed Exceptions to RuntimeExceptions in ParsedFileService so they're easier to work with after catching
- now deletes uploadedFiles from disk after storing in the database
- added transposeMatrix to parsedFileService
- enabled transposing of matrix
- put transpose functionality in transposeMatrixIfNeeded
- changed getDataMatrix to accept a parsedFile instead of a matrix in order to use rows and columns properties
- uploaded files now get collected by id instead of filename
- changed file_id to gridFSFile_id in UploadedFile
- made assayService mongo transactional
- started work on deleting uploaded files and parsedfiles
- added null check in getDataFromColumns
- added integration tests for uploadedFile/parsedFile
- added resources plugin to moduleStorage
- delete from uploaded file list now works
- download as well
- to circumvent mongo GORM relational problems, I embedded ParsedFile in UploadedFile, works like a charm -> parsedFile gets deleted when UploadedFile gets deleted
- setting UploadedFile.uploader to session.user upon saving
- Prepared project for deployment on server by changing in-place plugins to regular ones.
- increased version numbers here and there and straighted out dependencies
hopefully fixed package dependency issues