Working With Files
Introduction
Most types of analysis in Proteios SE require that you upload the files that are the basis of the work. Each user has a file directory on the server, and right under the root directory projects will have their own directory structures. It is recommended that you generate a directory structure for the projects such that peak lists are in one folder, search results in another etcetera.
The File/Directory View
The file/directory view shows the contents in the current directory in two tables, a directory table and a file table.
The directory table is used to navigate the file system, as clicking on a directory name changes the
view to the selected directory. Each table has a toolbar with a number of buttons for standard operations
for the items in the table. Some of the operations require that one or more items have been selected
by clicking the check box in the leftmost column before the toolbar button is pressed. The toolbar
also contains an "Extensions" button, which makes a pop-up menu appear, showing other operations
available for the table items. Extensions nearly always require items to have been preselected,
and will display an error message otherwise.
The complete file structure can be reached by selecting View -> My Files.
When you have an active project - select Files in the menu with the project name to show the project files. In the project root directory file view you can also find files and directories that have been shared to the active project. The files and directories with green background have been shared to the project but are not found within the normal directory structure.
Upload Demo Files
If you just want to test Proteios SE you can try the provided demo files. To add the demo files, activate
a project, select <Active Project> -> Files, and click the "Extensions" button in the toolbar
of the Files table to make the extensions pop-up menu appear. Select either
"Upload demo files for gel-based project" or "Upload demo files for non gel-based project",
depending on the type of project. These are two of the few extensions that do not require preselected items.
If all went fine you should now see a number of new folders (You have to be online for this to work).
Standard File Operations
Upload file
For normal file upload you can choose to upload files via the web interface or using ftp. The limitation of the web interface is that you have to upload files one by one which is not very practical for most projects. To upload a file via the web interface you should descend into the directory where you want the file to end up and select "Upload file".
If you have many files to upload it is usually best to use the ftp (instructions)
Moving files
To move files to different directory, select the files by clicking their checkboxes and press
the "Move" button. This takes you to a directory view, where you navigate into the target
directory you want to move the files to, and then press button "Next".
Changing file name and other file properties
Click the name of a file in the file view table to make the file properties form appear.
Currently name, description, and file type can be edited, and the changes saved by pressing
the "Save" button. File annotations can be inspected and edited in its own form tab.
Inspect contents of a file
To inspect raw contents of a file, click the name of a file in the file view table to make
the file properties form appear. If the file is a simple text file and not too large, its
contents can be inspected by pressing the "View" button. Image files of standard types
will have the image displayed in the file properties form. Files that are of other types
or too large to be shown in the web browser, can be downloaded for inspection on the local system.
Some files might be easier to inspect using specialized viewers, e.g. spectrum files might
be inspected using a viewer that displays the mass spectra in graphic mode. In this case,
click the checkbox for the file, and press the "Extensions" button in the toolbar
of the Files table to make the extensions pop-up menu appear, then check if there
is a suitable file viewer available.
Download a file
To download a file, click the name of a file in the file view table to make
the file properties form appear, then press the "Download" button to make
the download dialog appear.
Deleting files
To delete files, check the checkbox to the left of the files and press the "Delete" button. The files will then end up in the trashcan. You will not be able to upload another file with the same name to the directory until the trashcan has been emptied. To empty the trashcan, select View -> Home and press the "Empty trashcan" button.
Please note that it is currently not possible to delete files that are used by jobs in the job queue.
