Cyberduck

iRODS (RUG).cyberduckprofile

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  ~ Copyright (c) 2002-2017 iterate GmbH. All rights reserved.
  ~ https://cyberduck.io/
  ~
  ~ This program is free software; you can redistribute it and/or modify
  ~ it under the terms of the GNU General Public License as published by
  ~ the Free Software Foundation; either version 2 of the License, or
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  ~ This program is distributed in the hope that it will be useful,
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<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
    <dict>
        <key>Protocol</key>
        <string>irods</string>
        <key>Vendor</key>
        <string>renci</string>
        <key>Description</key>
        <string>RUG iRODS</string>
        <key>Hostname Configurable</key>
        <false/>
        <key>Port Configurable</key>
        <false/>
        <key>Default Hostname</key>
        <string>rdms-prod-icat.data.rug.nl</string>
        <key>Region</key>
        <string>rug:rootResc</string>
        <key>Default Port</key>
        <string>1247</string>
        <key>Authorization</key>
        <string>PAM</string>
    </dict>
</plist>

Once you are connected to the RDMS via Cyberduck, navigate through the Cyberduck interface to the desired target collection for uploading data. Your Home Drive is available via /rug/home/username@rug.nl, as well as any Team Drive or Project you are involved with under /rug/home/location.

Once you are in the desired collection, click on the upload button in the top bar (red outlined).

This will open a new window. Here you can navigate to the file(s) you want to upload and, once selected, you can start the upload by clicking the red outlined button.

The upload will now start and the window shown in the picture will appear.

If the upload finished successfully, Cyberduck will show the message below.

Finally, if you closed the window above, but would still want to check the history of your recent uploads, you can click on the “Transfers” button in the top bar (red outlined). The window will then reopen and show you the recent transfers.

To download data from the RDMS using Cyberduck, you need to follow a slightly different procedure compared to the upload of data. For instance, there is no download button at the top of the GUI, but the download functionality becomes available by right-clicking the file or folder you wish to download. So, navigate to what you wish to download using the File explorer of Cyberduck and right-click it. This will display the following menu.

Here you can select either of the three red underlined options: “Download”, “Download As”, or “Download To”. The first option, “Download”, will let you download the file in the specified Download directory, which you can set yourself by following the relevant step described in the Transfer Preferences section below.

The second option, “Download As”, will open up a window that will let you navigate through your local file structure and also rename the file you wish to download. Here you can potentially also change its file extension, though we recommend you do not do so. Finally, “Download To” will open a window that will let you choose where to save the file, but will not let you rename it.

Whichever option you choose, starting the download will open up the transfer window, where you can follow the progress of your download. If it succeeded, you will see the green icon displayed below and the confirmation that the download is complete. Should you have any trouble finding the file you downloaded in your local file structure, you can find it or open it by clicking on the download so it gets blue highlighted and then clicking one of the two icons in the red box.

Apart from up- or downloading files or entire folders manually in Cyberduck, you can also give the client the command to sync one of your local folders to a collection on the RDMS. The advantage of using Synchronize rather than Up- or Downloading the data, is that Synchronize will not transfer every file but only act on files that have been changed or that don't exist in the target directory. This will reduce the amount of data you will transfer at any one time. To Synchronize your folder, simply right-click the collection you wish to sync and the following menu will be displayed.

Click on “Synchronize…” (red underlined) and the next window will open. There you can navigate to the folder on your local machine that you wish to sync to the RDMS collection. Once you have selected it and confirmed, the transfer window will open and after a few seconds, this window will appear.

Among other things, the window will show the collection you wish to sync once again. Please make sure that it is indeed the collection you want to sync by checking the red-underlined entry. You can also check under “Details” that the “Remote File” and the “Local File” correspond to the collection and folder you selected. N.B.: Cyberduck talks of “files” here, but this obviously also applies to folders.

Finally, if you click the red box shown above, you will be given three options of how Cyberduck is going to handle your sync. Your options are:

• Download: Changes to the RDMS collection will be reflected in your local folder. Changes to your local folder will not be reflected in the RDMS collection.
• Upload: Changes to your local folder will be reflected in the RDMS collection. Changes to the RDMS collection will not be reflected in your local folder.
• Mirror: Any difference between the folders will be transferred, no matter if it was changed in your local folder or in the RDMS.

We suggest that you either use “Upload” or “Download” when using the Sync option, as you have a better handle of what is going to be changed. Please also keep in mind that Synchronize is a one time action. If you wish to sync your folder again, it will not happen automatically, but you will need to repeat the steps above.

In order to ensure that your transfer complete correctly, we suggest that you navigate to the “Edit” tab in the top menu and adjust your preferences. The picture below shows what you need to click to make the preference menu appear.

Once the menu is open, navigate to the transfer tab (red box) and click it. There are other preferences available at this stage, but we recommend that you only change how your transfers are handled.

This is not a necessary change, but if you are running into connection timeout issues with Cyberduck, navigate the the General tab in the “Transfer” window. Changing the option under “Transfer Files” from “Open Multiple Connections” to “Open Single Connection” can help solve that problem.

The second box in the image above (the one labelled “Downloads”) lets you set your preferred download folder. The default is the Download folder on your windows machine. If you wish to change this setting, just click on the “Choose…” button to the right and then navigate to the folder you wish to set as preferred.

Finally, the one option we recommend you turn on in your preferences is to always verify the checksum of your files, both in upload and in download. To do this, simply check the two boxes as shown in the picture.