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rdms:access:windows:cyberduck [2024/03/05 11:44] – Small adjustment to cyberducprofile to align better with the one inside the RDMS jelterdms:access:windows:cyberduck [2025/01/27 15:30] (current) – burcu
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 ====== Cyberduck ====== ====== Cyberduck ======
  
-Cyberduck is an open-source client for FTP, SFTP, and WebDAV available for macOS and Windows. It is pre-installed on the University Workspace (UWP) PCs and on the [[https://uwp.rug.nl/|virtual UWP]]. If you work on a user-managed workplace or any other device you can download Cyberduck from [[https://cyberduck.io/download/|here]]. +Cyberduck is an open-source client for FTP, SFTP, and WebDAV available for macOS and Windows. It is pre-installed on the University Workspace (UWP) PCs and on the [[https://uwp.rug.nl/|virtual UWP]]. If you work on a user-managed workplace or any other device you can [[https://cyberduck.io/download/|download Cyberduck]] from its official website. 
-{{ :rdms:access:cyberducklogo.png?100|}}+{{ :rdms:access:cyberducklogo.png?direct&100|}}
  
 Cyberduck is a solution to transfer files to and from the RDMS. To manage data, metadata, users, and projects on the RDMS, you need to connect to the [[rdms:webapp|RDMS WebApp]]. Cyberduck is a solution to transfer files to and from the RDMS. To manage data, metadata, users, and projects on the RDMS, you need to connect to the [[rdms:webapp|RDMS WebApp]].
  
-Cyberduck can connect to the RDMS both by using a **WebDAV** and a **native iRODS** protocol. +To access the Default zone, Cyberduck can connect to the RDMS using both the **WebDAV** and the **native iRODS** protocol. For the [[https://wiki.hpc.rug.nl/rdms/solution/multizone|Sensitive Data (SD) zone]], you should use the **RDMS SD Cyberduck Profile**. Instructions om how to configure Cyberduck for each case are provided below.
  
 **Notes:**  **Notes:** 
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   * **Password:** Your UG password   * **Password:** Your UG password
  
-{{ :rdms:access:cyberduckinlog.png?800 | }}+{{ :rdms:access:windows:cyberduck_webdav_new.png?direct&500 |}}
  
 +**Note:** If you experience issues with this, be sure that you specified your username in lowercase. The login to the RDMS is case sensitive!
  
  
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 ++++ ++++
  
-If everything went right, you will see the login screen below.  It will connect you to the RDMS "rug" zone using the native iRODS protocol. Simply insert your UG email address and associated password to connect to the system. It should have also created an editable bookmark for your connection.+If everything went right, you will see the login screen below.  It will connect you to the RDMS "rug" zone using the native iRODS protocol. Simply insert your UG email address (lowercase!) and associated password to connect to the system. It should have also created an editable bookmark for your connection. 
 + 
 +{{ :rdms:access:windows:cyberduck_rug_connection.png?direct&500 |}} 
 + 
 +===== Configuration of Cyberduck to access the RDMS SD Zone ===== 
 + 
 +In order to access the RDMS SD zone, you need to first download the RDMS Sensitive data zone Cyberduck profile directly by clicking on the link below or by copying the content to a text editor of your choice and then save as a ''*.cyberduckprofile'' file. Afterwards, double click the downloaded/created ''*.cyberduckprofile'' file to install add it to Cyberduck. Then, click **Open Connection**, select the RDMS SD Cyberduck Profile protocol, and configure the login credentials as follows: 
 + 
 +++++ Cyberduck profile for the Sensitive Data Zone | 
 +<file xml RDMSsd.cyberduckprofile> 
 +<?xml version="1.0" encoding="UTF-8"?> 
 +<!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>sdrug</string> 
 +        <key>Description</key> 
 +        <string>RDMS (sdrugZone)</string> 
 +        <key>Default Nickname</key> 
 +        <string>RDMS sdrugZone zone</string> 
 +        <key>Default Hostname</key> 
 +        <string>store-sd.data.rug.nl</string> 
 +        <key>Hostname Configurable</key> 
 +        <false/> 
 +        <key>Region</key> 
 +        <string>sdrugZone:rootResc</string> 
 +        <key>Default Port</key> 
 +        <string>1247</string> 
 +        <key>Port Configurable</key> 
 +        <false/> 
 +        <key>Username Configurable</key> 
 +        <true/> 
 +        <key>Default Path</key> 
 +        <string>/sdrugZone/home</string> 
 +        <key>Path Configurable</key> 
 +        <true/> 
 +        <key>Authorization</key> 
 +        <string>PAM</string> 
 +    </dict> 
 +</plist> 
 +</file> 
 +++++ 
 + 
 +  * **Protocol:** ''RDMS SD Cyberduck Profile'' 
 +  * **Port:** ''1247'' 
 +  * **Server:** ''store-sd.data.rug.nl'' 
 +  * **Username:** ''<username>@rug.nl'' 
 +  * **Password:** Your UG password 
 + 
 +{{ :rdms:access:windows:cyberduck_sd1.png?direct&600 |}} 
 + 
 +**Note:** If you experience issues with this, please make sure that you specified your username in lowercase. The login to the RDMS is case sensitive!
  
-{{ :rdms:access:windows:cyberduck_new.png?direct&700 |}} 
 ===== Transferring Data to and from the RDMS via Cyberduck ===== ===== Transferring Data to and from the RDMS via Cyberduck =====
  
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 Once you are in the desired collection, click on the upload button in the top bar (red outlined). Once you are in the desired collection, click on the upload button in the top bar (red outlined).
-{{ :rdms:access:windows:cyberduck_step_1.png?600 |}}+{{ :rdms:access:windows:cyberduck_step_1.png?direct&600 |}}
  
  
 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. 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.
-{{ :rdms:access:windows:cyberduck_step_2.png?600 |}}+{{ :rdms:access:windows:cyberduck_step_2.png?direct&600 |}}
  
 The upload will now start and the window shown in the picture will appear. The upload will now start and the window shown in the picture will appear.
-{{ :rdms:access:windows:cyberduck_step_3.png?600 |}}+{{ :rdms:access:windows:cyberduck_step_3.png?direct&600 |}}
  
 If the upload finished successfully, Cyberduck will show the message below. If the upload finished successfully, Cyberduck will show the message below.
-{{ :rdms:access:windows:cyberduck_step_4b.png?600 |}}+{{ :rdms:access:windows:cyberduck_step_4b.png?direct&600 |}}
  
 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. 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.
  
-{{ :rdms:access:windows:cyberduck_step_5.png?600 |}}+{{ :rdms:access:windows:cyberduck_step_5.png?direct&600 |}}
 ++++ ++++
 ==== Download ==== ==== Download ====
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 ++++ Click to display section | ++++ Click to display section |
 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. 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.
-{{ :rdms:access:windows:down_1.png?600 |}}+{{ :rdms:access:windows:down_1.png?direct&600 |}}
  
 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 [[https://wiki.hpc.rug.nl/rdms/access/windows/cyberduck#transfer_preferences|Transfer Preferences]] section below. 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 [[https://wiki.hpc.rug.nl/rdms/access/windows/cyberduck#transfer_preferences|Transfer Preferences]] section below.
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 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. 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.
-{{ :rdms:access:windows:down_2.png?600 |}}+{{ :rdms:access:windows:down_2.png?direct&600 |}}
  
 ++++ ++++
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 ++++ Click to display section | ++++ Click to display section |
 To synchronize your folder, simply right-click the collection you wish to sync and the following menu will be displayed. To synchronize your folder, simply right-click the collection you wish to sync and the following menu will be displayed.
-{{ :rdms:access:windows:sync_1.png?600 |}}+{{ :rdms:access:windows:sync_1.png?direct&600 |}}
  
 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. 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.
-{{ :rdms:access:windows:sync_2.png?600 |}}+{{ :rdms:access:windows:sync_2.png?direct&600 |}}
  
 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 and the local files correspond to the collection and folder you selected. **N.B.**: Cyberduck talks of "files" here, but this obviously also applies to folders. 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 and the local files correspond to the collection and folder you selected. **N.B.**: Cyberduck talks of "files" here, but this obviously also applies to folders.
-{{ :rdms:access:windows:sync_3.png?600 |}}+{{ :rdms:access:windows:sync_3.png?direct&600 |}}
  
 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: 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:
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 In order to ensure that your transfer completes correctly, we suggest that you navigate to the ''Edit --> Preferences...'' tab in the top menu and adjust your preferences. The picture below shows what you need to click to make the preference menu appear. In order to ensure that your transfer completes correctly, we suggest that you navigate to the ''Edit --> Preferences...'' tab in the top menu and adjust your preferences. The picture below shows what you need to click to make the preference menu appear.
-{{ :rdms:access:windows:pref_1.png?600 |}}+{{ :rdms:access:windows:pref_1.png?direct&600 |}}
  
 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. 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.
-{{ :rdms:access:windows:pref_2.png?600 |}}+{{ :rdms:access:windows:pref_2.png?direct&600 |}}
  
 This is not a necessary change, but if you are running into connection timeout issues with Cyberduck, navigate the the "General" tab in the "Transfers" window. Changing the option under "Transfer Files" from "Open Multiple Connections" to "Open Single Connection" can help solve that problem. This is not a necessary change, but if you are running into connection timeout issues with Cyberduck, navigate the the "General" tab in the "Transfers" window. Changing the option under "Transfer Files" from "Open Multiple Connections" to "Open Single Connection" can help solve that problem.
-{{ :rdms:access:windows:pref_3.png?600 |}} 
  
-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.+Furthermore, be sure that you **disable the option for segmented downloads** as this can introduce issues with your downloads.  
 + 
 +{{ :rdms:access:windows:pref_3_new.png?direct&600 |}} 
 + 
 +In the same section of Cyberduck's preferences, you can also adjust your default download folder. If you wish to change the current setting, just click on the ''Choose...'' button to the right and then navigate to the folder you wish to set as preferred download destination.
  
 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, otherwise only the size is used. To do this, simply check the two boxes as shown in the picture. 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, otherwise only the size is used. To do this, simply check the two boxes as shown in the picture.
-{{ :rdms:access:windows:pref_4.png?600 |}}+{{ :rdms:access:windows:pref_4.png?direct&600 |}}
  
 ++++ ++++