Managing Files

Files in the Research Workspace (RW) are stored and managed just like on your computer, in a hierarchy of folders. Almost everything you can do on your own computer to organize files, you can do in the RW.

Note

For more information on organizing and managing files, please see Axiom Data Science’s Best Practices for Data Management.

File List

You can access a project’s file list by selecting a project from your project list. The RW can accept and store any type of file, from raw CTD hex files to Microsoft Access databases. The file list shows the contents of the currently selected project and folder. If it’s a new project, there will be a default Files folder with nothing in it. If you’ve uploaded files, each line of the file list shows a checkbox, the metadata icon, the filename, filesize, who uploaded it, and when the file was last updated.

Note

When you open the file list, the first folder in the folder list is selected by default, even if that folder is empty.

Upload Files

One of the most important things you’ll need to do in the RW is upload files to analyze, publish, or archive. There are two ways to upload your files.

Add Files Button

To upload files using the green add files button , follow these steps:

1. Select the folder where you want the files to be stored.
2. Click the green Add files button.
3. Use the dialog to navigate to the files stored on your computer, and select the files. Use Shift + click to select multiple files listed adjacently, or Ctrl + click to select multiple files that are distributed throughout the directory.
4. Select Open to begin the upload.

Drag and Drop Files

You can also upload files by dragging and dropping them into your browser window:

1. Select the folder where you want the files to be stored.
2. Navigate to the file or files stored on your computer and select them. Use Shift + click to select multiple files listed adjacently, or Ctrl + click to select multiple files that are distributed throughout the directory.
3. Drag and drop the selected file(s) from your computer into the RW browser window.

Tip

Using the RW in the Chrome browser allows you to drag and drop entire directories into the RW, and it preserves the directory structure. Unfortunately, other browsers do not support this feature at this time.

File Versioning

If you’re updating an existing file, you can let the RW do version control for you. Don’t delete the original, just upload the new version (without changing the filename). The updated column will show the new time, and clicking on the time will bring up a list of previous versions.

Tip

You can click and drag to reorder the versions, putting a previous one back on top.

Create New Files

You can create two types of new, blank documents directly in the RW using the new file drop-down box :

• Jupyter notebooks: Create a new Jupyter notebook by using the New file dropdown and choosing Jupyter notebook.
• Text files: Create a new, blank, text file by selecting the New file dropdown and choosing Text file. Text files can be used as a place to store cut-and-pasted text, notes to collaborators, a scratch pad, or ancillary code or data for your Jupyter notebook.

Note

When creating new files, try to use logical and consistent naming conventions. For more information on how to use file naming to help you organize and manage your data, please see Axiom Data Science’s Best Practices for Data Management.

Rename Files

To rename file, follow these steps:

1. Click the caret (grey down arrow) that appears when you hover to the left of the file name.
2. Select Rename from the drop down menu.
3. Enter a name in the file text box field.
4. Hit the green checkmark button to save the change, or the red X button to cancel.

Move Files

To move files to another RW folder or project, follow these steps:

1. Select the checkboxes next to the files you want to move.
2. In the Actions dropdown, select Cut files.
3. Navigate to the new folder or project where the files are going.
4. Use the Actions dropdown and select Paste files.

Tip

If the folders you are moving files between are both in the same project, you can also just use the checkboxes to select the files, then drag and drop them into their new location in the folder list.

Download files

There are several options to download files in the file list.

Download Individual Files

To download individual files, click on the filename in the file listing. The file should begin downloading immediately. Groups of files will be zipped together by the RW before your download begins, up to a maximum zipped size of 2 GB.

Tip

If your browser tries to open and view the file immediately, but you want to save it (this often happens for image files and PDFs), right click on the file and select Save as....

Download Groups of Files

To download a group of files, follow these steps:

1. Check the boxes to the left of the filename next to the files you want in the file list.
2. Select the actions dropdown box .
3. Select Download [n] files, where [n] is the number of files selected.
4. The files will be zipped together and begin downloading, up to a maximum zipped size of 2GB.

Download All Files in a Folder

To download all of the files in the present directory, there are 2 options:

Option 1

1. From within your project, make sure that none of the file boxes is selected, and select the actions dropdown box .
2. Select Download All.
3. The files will be zipped together and begin downloading, up to a maximum zipped size of 2GB.

Option 2

1. From within your project, select the check box in the file list header, which will select all files.
2. Select the actions dropdown box .
3. Select Download [n] files, where [n] is the number of files selected.
4. The files will be zipped together and begin downloading, up to a maximum zipped size of 2GB.

Add File Metadata

File-level metadata provides the most specific tier of metadata and describes the content of each file itself. File metadata content is more descriptive than folder metadata, and focuses on details that typically vary among files of different types or data that were collected in different ways. File-level metadata covers elements specific to the data contained within the file and how it was collected, such as dates, specific locations, research methods, processing, and citations.

To create file metadata, follow these steps:

1. In the project files view, click on the grayed-out metadata icon next to the file for which you want to add metadata.
2. A new record will open to the Resource Overview section within the metadata editor.

Refer to the Metadata Editor documentation for help generating a metadata record for the file.

Delete Files

You can delete files two ways following these steps:

Option 1

1. Select the checkbox next to the file name.
2. Press the red delete button .

Option 2

1. Click the caret (grey down arrow) that appears when you hover to the left of the file name.
2. Select Delete from the drop down menu.

Note

Deleted files will be sent to the trash for 30 days before they are permanently deleted. From the trash, you can either recover files or permanantly delete them.

Tip

More than one file can be deleted at a time by selecting multiple checkboxes, or clicking the uppermost checkbox to select all files within a folder.

Recover Files

To recover deleted files from the trash and return them to a project, follow these steps:

1. Under the actions dropdown menu , select View Trash to see the recently deleted files.
2. Select the checkboxes next to the files you want to recover.
3. Press the green Recover button.

Note

Recovering files will send them back to the folder from which they were deleted. If that folder has also been deleted, the files will go to the first folder in the project’s folder list.

Permanently Delete Files

To permanantly delete folders from the RW without waiting for 30 days:

1. Delete the files from the project.
2. Use the actions dropdown menu and select View Trash.
3. Select the checkboxes next to the filenames you want to remove.
4. Use the Delete forever button.