Add a demo project extension for non-gel based projects

[Gregory Vincic]

There should be some demo data for testing non-gel based projects

[olle]

Ticket accepted.

[olle]

Traceability note:

• Uploading of demo data for gel based projects was updated in Ticket #712 (Make "Upload Demo Files" into a context enabled action).
• Uploading of demo data for gel based projects was updated in Ticket #734 (Routine for uploading demo files should be made more robust and forgiving).

[olle]

Design discussion.

• The design for uploading of demo files for non gel-based projects will be based on that for gel-based projects, which is managed by class UploadDemoFiles, and has been updated in Ticket #734 (Routine for uploading demo files should be made more robust and forgiving).
• The demo files for non gel-based projects will be based on the files in archive ​http://www.proteios.org/trac/htdocs/downloads/Met_Mol_Biol_2011_Data/Quantitative_LC-MS_example_data.zip, that contains peaklist, search parameter, Mascot search result, and X!Tandem search result files.
• The peaklist files in the archive have names
  
  TMT6-plex_fraction1.mzData
TMT6-plex_fraction2.mzData
  
  , which are not suitable for hits import using the default regex pattern ".+\_(.+)\..+" to parse the fraction id from the peaklist filename, since this would result in "fraction1" and "fraction2", respectively, which have 9 characters while only 8 are allowed for a fraction id value in the database. The peaklist filenames will therefore be changed to
  
  TMT6-plex_fraction_1.mzData
TMT6-plex_fraction_2.mzData
  
  , respectively, which with the default regex pattern will result in fraction id values "1" and "2". Since the search result files contain the name of the used peaklist file, the former should be updated to be consistent with the new peaklist file names.
• The same server base directory will be used for demo files for non gel-based projects as for gel-based projects, ​http://www.proteios.org/trac/downloads/demoProjectFiles/, but to avoid mix-up with the latter, the new files will be placed in directory non_gel-based_data/, which will have three sub-directories for the different types of file:
  
  non_gel-based_data/peak_lists/
non_gel-based_data/search_parameters/
non_gel-based_data/search_results/ (containing both Mascot and X!Tandem result files)
  
  
• In analogy with the case for uploading of demo files for gel-based projects, the uploaded files will be placed in sub-directories to the project directory of the active project, depending on type of file:
  
  Peaklist files/
Search parameter files/
Mascot files/
X!Tandem files/
  
  
• Since the current set of demo files for non gel-based projects contains more and larger files than for gel-based projects, uploading of the demo files will be performed as a job. The files will be uploaded to the project that was active when the job was created.
• Even though the demo files for non gel-based projects are larger than corresponding files for gel-based projects, the former files are not huge according to current standards (the largest is 25.3 Mb), and they will therefore be stored uncompressed when uploaded to Proteios SE.

[olle]

(In [4138]) Refs #733. First version of uploading of demo files for non gel-based projects:

1. New class/file action/project/UploadDemoFilesNonGelBased.java in client/servlet/ added. It checks that an active project exists, and then creates a job using new plug-in class UploadDemoFilesNonGelBasedPlugin. The project is transferred to the job as a job parameter.

2. New class/file plugins/UploadDemoFilesNonGelBasedPlugin.java in plugin/ added. It creates new target directories in the project directory, if needed, and uploads the demo files to them.

[olle]

Tests:

• Setup:
  A new non gel-based project was created, and made the active project. In the Files form for the active project, the File context extension "Upload demo files for non gel-based project" was selected.
  Result:
  A job was created, that ended successfully with the message "10 demo files uploaded". Inspection showed that the expected four directories with 10 files had been created in the project directory of the project that was active when the job was created, and the files had the expected attributes.
• Setup:
  In the same project, directory "Search parameter files" with its two files were deleted, and one of the four X!Tandem result files was also deleted. In the Files form for the active project, the File context extension "Upload demo files for non gel-based project" was selected.
  Result:
  A job was created, that ended successfully with the message "3 demo files uploaded, 7 files already existing". Inspection showed that the deleted directory and files had been created and uploaded, and no other directories or files created or uploaded.

Conclusion: The tests gave the desired results and the tests therefore passed with successful result.

[olle]

Ticket closed as the requested functionality has been added.

[olle]

(In [4369]) Refs #787. Refs #733. Class/file plugins/UploadDemoFilesNonGelBasedPlugin.java in plugin updated in private method void addSearchParameterFiles(Directory parentDir) to set appropriated file type for copied search parameter files.