File Management¶
The Files tab allows you to manage:
files in your tale workspace or home folder
Tale Workspace¶
The Tale Workspace folder is the primary storage area (or folder) for
all files associated with a tale. This folder is available in your running
tale environment as workspace.
Tale workspace and menu¶
Workspace Operations¶
Common operations include:
Upload files or folders from your local machine
Create, rename, move, remove, copy, download files and folders
Copy or move files between tales
Selecting a folder or file will present a menu with the following options:
Move To: move a file or folder
Rename: rename a file or folder
Share: share a file or folder with a user or group
Copy: copy a file or folder
Download: download a file or folder
Remove: remove a file or folder
Home Folder¶
The Home folder is your personal workspace in the Whole Tale system. You can perform most common operations including uploading, creating, moving, renaming, and deleting files and folders.
Your Home folder is mounted into every running tale instance with full read-write permissions. This means that you can access and manage files from both the Whole Tale dashboard and within tale environments. This is in contrast to the Data folder described below, which is limited to read-only access.
External Data¶
The External Data folder contains references to data you’ve registered in the system for use with the tale. This data is meant to be read only and can only be added from external sources. With this folder you can:
Register data from external sources (e.g., via DOI or URL)
Select and add registered data to a Tale
Supported Data Repositories¶
The current supported repositories that you can register data from are
Zenodo: A general purpose research data repository.
Dataverse: An open source research data repository platform with 35 installations worldwide including the flagship Harvard Dataverse.
Globus: A service geared towards researchers and computing managers that allows custom APIs, data publication, and file transfer.
DataONE: A federation of data repositories with a focus on scientific data. A list of participating member nodes can be found on the member node information page.
5. DERIVA: “DERIVA <http://isrd.isi.edu/deriva/>`_ is an asset management platform with a number of deployments. Support for DERIVA in WholeTale is being tested using data from The Pancreatic β-cell Consortium.
Adding Data¶
Files and folders cannot be uploaded to the External Data folder directly. To encourage reproducibility, only data registered from external resources and associated with a tale will be available in the External Data folder.
To register data from an external resource, use the data registration dialog, shown below.
The data registration dialog allows you to search by DOI and ingest data into Whole Tale.¶
To access this dialog, navigate to the External Data folder by clicking the link icon below the home directory folder.
A user’s External Data folder, populated with data that was registered from external sources.¶
The blue plus icon will open the registration dialog where you can find and register your data. You’ll need to have either the DOI or data package URL to find the data.
Adding Data From DataONE¶
Data packages from DataONE can be integrated into Whole Tale by searching for the DOI of the package or by pasting the URL into the search box in the registration modal.
By DOI
Consider the following package. Visiting the package landing page we can see that the DOI is “doi:10.18739/A29G5GD0V”. To register this data package using the DOI, open the registration dialog and paste the DOI into the search box. Click “search” and check that the correct package was found. Click “Register” to begin data registration.
A dataset that was found by searching for the DOI.¶
By URL
The URL of the data package can also be used to locate the package instead of the DOI. In the previous example, pasting “https://search.dataone.org/#view/doi:10.18739/A29G5GD0V” into the search box will give the same data package which can subsequently be registered.
A dataset that was found by searching with the package’s DataONE url.¶
Adding Data From Dataverse¶
Whole Tale allows to register data from all 35 public Dataverse installations. Support for additional installations can be added per user request. Similarly to DataONE, data can be registered both by providing DOI or direct URL into the search box of the registration modal.
By DOI
DOIs may be specified for either datasets or individual files. For example:
Dataset: doi:10.7910/DVN/TJCLKP
By URL
URLs may be specified for either datasets or individual files using the web or Data Access API formats. For example:
Adding Data From Globus¶
Data can also be retrieved from Globus by specifying the DOI of the package, as done in the DataONE case.
Note
Only the Materials Data Facility is currently supported.
By DOI
The DOI of the dataset can be found on the dataset landing page. For example, the Twin-mediated Crystal Growth an Enigma Resolved package has DOI 10.18126/M2301J. This DOI should be used in the data registration dialog when searching for the dataset.
Adding Data From DERIVA¶
Data from a DERIVA deployment can be added by browsing to a dataset in the DERIVA user interface and clicking on the Export button in the upper right corner of the screen:
Clicking the export button triggers a drop-down menu, where an option to export to WholeTale can be selected:
Once the export is initiated, the DERIVA backend will package the dataset and redirect to WholeTale, where the dataset can be imported.
Adding Data From The Filesystem¶
Files and folders cannot be uploaded to the Data folder directly. To encourage reproducibility, only data registered from external resources or associated with a tale will be available in the Data folder. The data can however, be uploaded to the Home directory.