When you create an account in BioQuery you are given a folder on the BioQuery server in which to save your Searches and Results. You can access this folder through the File Manager. The File Manager can be used to open, rename, move, copy, and delete files from the BioQuery server. It can also be used to create new Folders to help you organize your Searches and Results.
The File Manager is displayed on the left side of the screen, and can be 'opened' or 'closed' with the use of a button in the toolbar labeled 'Show File Manager' or 'Hide File Manager'. Pressing this button toggles whether the File Manager is visible, or whether it has 'closed' into the left side of the screen. You can also close the File Manager by pressing the button with the 'X' in the top right corner of the File Manager, or by using the 'Window' menu in the menubar at the top of the program.
The File Manager uses a 'tree' structure to show all of the folders and files saved to the server. When you first create an account, there is only one folder: your username folder. This is always the top-level folder for your account, and you cannot rename it. You can create new folders under it and save files to any folder in the File Manager.
The File Manager contains 3 things:
Folders are often displayed 'closed'. That is, what is inside of them is not being shown. Click the symbol on the left side of the folder to open it. Click it again to shut it. You can also open and close folders by double-clicking on them. If you can't find a file, make sure you have opened all of your folders and that everything is visible before you panic. Then panic.
Search Files are from any Search that you created and saved. Give them descriptive names, the 'Q' icon looks the same regardless of which databases they come from.
The Results Files are simple text files, or html pages. You must create and submit a Search to create a Results file.
You will not see any Search or Results files in your account until you create and save them. Remember to save your files before closing the program!
Most of the options for working with files are available in a by right-clicking (or control-click) on the filename. If an option is greyed out, you cannot perform that operation on that type of file or folder.
Some operations only work on files that are currently open, while others only work on files that are saved on the server and are NOT open.
Close file, Save, and Save As only work on OPEN files. These functions are located under the 'File' menu, and can also be found in a popup menu when you right-click (control-click) on the Tab (in the right side of the window) of any open file. These operations always apply to whatever open file is visible (has the top Tab) on the right. It does not matter what filename is selected in the File Manager.
Create Folder, Open File, Copy File, Move File, Rename File, and Delete File only work on SAVED files. These functions are only found by right-clicking (control-click) on a file or folder in the File Manager window. These operations are always applied to whatever file or folder is selected in the File Manager, and it does not matter what file is currently diplayed in the Tab on the right. Move and Delete will not work if the file is currently open, but the other functions will.
If you get an error trying to open a file, you may be having trouble contacting the server. Try logging out and logging back in (from the 'Account' menu).
Any file that is open (that is, it has a tab on the right) can be closed either of 2 ways:
Any View that get's it's own Tab can be saved as a file. This can be either a Search or a set of Results. When a Search is saved, all of the Search History lines, as well as all of it's settings and automation settings are saved. The results in the Results Box at the bottom ARE NOT SAVED. To save those results, you must click either the 'Edit Results' or 'Save Results' buttons in the Results Box. This will open the results in their own view, which can be saved as a text or html file. Anything you type or any modifications you make to a Results View will be saved, exactly as you typed them.
To save a File, make sure it's View is visible on the right (it's tab is on top). Click on the 'File' menu and select 'Save' or 'Save As'. If you have never saved this file before, they will both do the same thing: you will be prompted to enter a filename and choose a folder in your account, and the File will be saved under that name to that folder. This may change the name shown in the tab, since that is the file name. You can also right-click (control-click) on the tab for any View. You will be given the option to 'Save' and 'Save As' in the popup menu.
Please note: if a file has not been modified, the 'Save' and 'Save As' options will be greyed out. They will be reactivated as soon as you alter the file in any way.
If the file has never been saved before, they do the same thing. If the file has been previously saved, 'Save' will save the newly modified file over the old one without asking any questions. 'Save As' will always ask you to tell it the filename and location to save the file, and will ask you before it overwrites any existing files.
Files can be saved to the local computer as well as to the BioQuery server. Autosubmit does not work for local copies of Searches, so make sure there is also a copy saved to the BioQuery server if the Auto-Submit feature is turned on. Search files can only be opened by BioQuery, but Results files are usually text or HTML and can thus be opened by a web browser or other programs. It is a good idea to make a local backup of important work, and also leave a copy on the BioQuery server.
To Save a File Locally, make sure it's View is visible on the right (it's tab is on top). Click on the 'File' menu and select 'Local Copy', then select 'Save Locally'. A File Chooser will open for your local hard drive. Select a destination and filename and click 'OK'. Also save a copy of your Search to the BioQuery server if you want to receive automatic updates of new data.
To Open a local file on your computer, click on the 'File' menu and select 'Local Copy', then select 'Open Locally'. A File Chooser will open for your local hard drive. Select the file you want to open and click 'OK'.
See Saving a File.
See Saving a File.
To create a new folder, right-click (control-click) on the folder name in the File Manager and select 'Create Folder' from the popup menu. You will be asked to type in a new folder name, and the new folder will be created under the one that is selected. You cannot create a folder under a file, only under another folder.
You also have the option of creating new folders when you first Save a file or do a Save As, so you can immediately save the file into the newly created folder.
You can move a file from one folder to another.
To move a file, right-click (control-click) on the file name in the File Manager and select 'Move File' from the popup menu. A window will open that lets you select a destination folder for the file. Click on the destination, and then click the 'Move File' button at the bottom. The file will move from it's current folder to the new one. You cannot move a file while it is open. Close the file first, then move it and reopen it.
You can make a copy of any file on the server. This allows you to create backup copies of important files before you modify them, and may be useful for using an existing Search as the basis for creating a new one. You can change the name of the file when you copy it if you wish.
Please note: if you copy a Search that has the Automatic-Update feature turned on, you will create a SECOND Search that has the Automatic-Update feature turned on. You should either change the new Search file or turn it's update feature off. Otherwise, you will receive TWO copies of the same automated Search.
To copy a file, right-click (control-click) on the file name in the File Manager and select 'Copy File' from the popup menu. A window will open that lets you select a destination folder for the file, and change the name if you wish. Click on the destination, and then click the 'Copy File' button at the bottom. A new copy of the file will be created. New copys automatically get the same extension (the last 3 letters of the name after the period . ) as the original file. This part of the name tells BioQuery what type of file it is, and should not be changed.
To change the name of a file, right-click (control-click) on the file name in the File Manager and select 'Rename File' from the popup menu. You will be asked to enter a new file name. Type in the name click 'OK'.
A note about file extensions:
The ending part of the file name (the last 3 letters of the name after the period . ) tells BioQuery what type of file it is, and should not be changed. When you rename a file, you can add the extension to it, or you can change the extension. BioQuery will then ask you if you want to automatically keep the original extension. Choose 'YES'. This will make sure your files continue to work properly. If you choose 'NO', then your file will always be treated as a text file, and Searches will no longer work until you change the extension back to '.qry'. This will also prevent the Automatic-Update feature from working for that Search.
You can (and should) delete unused or unwanted files from the Server.
To delete a file, right-click (control-click) on the file name in the File Manager and select 'Delete File' from the popup menu. You will be asked to confirm the delete. Make sure the program is deleting the correct file and press the 'DELETE' button. The file is now permanently gone.
Please note: There is NO trashcan or recycle bin for the BioQuery File Manager! Deleted files are removed permanently, and can never be recovered. Be careful before pushing the button labeled 'DELETE'.
You can also delete a folder in the same manner as a file. This will delete the folder and all other files and folders within it! Be VERY VERY careful when doing this. Make sure you know what is in the folder, and that you are positive that everything inside it should be deleted. You can never get these files back.
You cannot delete a file while it is open. Close the file first, then delete it from the server.