Opened 10 years ago

Closed 10 years ago

#787 closed (fixed)

Search parameter file type

Reported by: Fredrik Levander Owned by: olle
Milestone: Proteios SE 2.17.0 Keywords:
Cc:

Description

Search parameter sets should have an own filetype to avoid confusion.

Change History (14)

comment:1 Changed 10 years ago by olle

Status: newassigned

Ticket accepted.

comment:2 Changed 10 years ago by olle

Traceability note:

  • Starting X!Tandem searches from Proteios was introduced in Ticket #362 (Run X!Tandem from Proteios).
  • Starting OMSSA searches from Proteios was introduced in Ticket #471 (Searching OMSSA from Proteios SE).
  • Starting Mascot searches from Proteios was introduced in Ticket #534 (Mascot GUI).

comment:3 Changed 10 years ago by olle

Design note:

  • A file type for OMSSA search parameters FileType.OMSSA_PARAMETERS was already introduced in Ticket #471 (Searching OMSSA from Proteios SE), changeset [2942].

comment:4 Changed 10 years ago by olle

(In [4364]) Refs #787. Refs #362. New X!Tandem search parameter file type FileType.XTANDEM_PARAMETERS added.

comment:5 Changed 10 years ago by olle

(In [4365]) Refs #787. Refs #534. New Mascot search parameter file type FileType.MASCOT_PARAMETERS added.

comment:6 Changed 10 years ago by olle

Design update:

  • When a new search parameter set is created, the corresponding parameter file should be set to the correct file type (currently no file type is set).

comment:7 Changed 10 years ago by olle

(In [4366]) Refs #787. Refs #362. Refs #363. When a new X!Tandem search parameter set is created, the corresponding parameter file is set to file type FileType.XTANDEM_PARAMETERS:

  1. Class/file action/xTandemInput/AddXTandemParameterSetStorage.java in client/servlet/ is updated in protected method void runMe() to cover the case when a new search parameter set is created using "Save".
  1. Class/file action/xTandemInput/SaveXTandemParameterSetStorage.java in client/servlet/ is updated in protected method void runMe() to cover the case when a new search parameter set is created using "Save As...".

comment:8 Changed 10 years ago by olle

(In [4367]) Refs #787. Refs. #534. When a new Mascot search parameter set is created, the corresponding parameter file is set to file type FileType.MASCOT_PARAMETERS:

  1. Class/file action/mascot/AddMascotParameterSetStorage.java in client/servlet/ is updated in protected method void runMe() to cover the case when a new search parameter set is created using "Save".
  1. Class/file action/mascot/SaveMascotParameterSetStorage.java in client/servlet/ is updated in protected method void runMe() to cover the case when a new search parameter set is created using "Save As...".

comment:9 Changed 10 years ago by olle

(In [4368]) Refs #787. Refs #471. When a new OMSSA search parameter set is created, the corresponding parameter file is set to file type FileType.OMSSA_PARAMETERS:

  1. Class/file action/omssa/AddOMSSAParameterSetStorage.java in client/servlet/ is updated in protected method void runMe() to cover the case when a new search parameter set is created using "Save".
  1. Class/file action/omssa/SaveOMSSAParameterSetStorage.java in client/servlet/ is updated in protected method void runMe() to cover the case when a new search parameter set is created using "Save As...".

comment:10 Changed 10 years ago by olle

Design update:

  • When files with demo data are uploaded via file extensions for gel-based and non gel-based projects, search parameter files should be set to the correct file type (currently no file type is set).

comment:11 Changed 10 years ago by 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).
  • Uploading of demo data for non gel-based projects was introduced in Ticket #733 (Add a demo project extension for non-gel based projects).

comment:12 Changed 10 years ago by olle

Design discussion.

Current design:

  • Uploading of demo data for gel-based projects is managed by class/file action/project/UploadDemoFiles.java in client/servlet/.
  • Uploading of demo data for non gel-based projects is managed by class/file action/project/UploadDemoFilesNonGelBased.java in client/servlet/. The action servlet starts a job managed by class/file plugins/UploadDemoFilesNonGelBasedPlugin.java in plugin/ to perform the actual file copying, since the files are larger than for the gel-based case.

Design update:

  • Currently no search parameter demo files are uploaded for gel-based projects, while for non gel-based a Mascot and an X!Tandem parameter file are uploaded. Therefore only the plugin class UploadDemoFilesNonGelBasedPlugin needs to be updated to set the file type for search parameter files.

comment:13 Changed 10 years ago by 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.

comment:14 Changed 10 years ago by olle

Resolution: fixed
Status: assignedclosed

Ticket closed as the requested additions have been made.

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