Cyberduck

RDMS.cyberduckprofile

<?xml version="1.0" encoding="UTF-8"?>
<!--
  ~ 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
  ~ (at your option) any later version.
  ~
  ~ This program is distributed in the hope that it will be useful,
  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  ~ GNU General Public License for more details.
  -->
 
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
    <dict>
        <!-- DO NOT CHANGE. This is the purpose of the profile-->
        <key>Protocol</key>
        <string>irods</string>
 
        <!-- Undocumented for CLI, the URI prefix, e.g., rug:// -->
        <key>Vendor</key>
        <string>rug</string>
 
        <!-- Name of the profile -->
        <key>Description</key>
        <string>RDMS (rug) 9.4.0+, iRODS 4.3.2+</string>
 
        <!-- Default name of bookmark -->
        <key>Default Nickname</key>
        <string>RDMS rug zone</string>
 
        <!-- iRODS hostname settings -->
        <key>Hostname Configurable</key>
        <false/>
        <key>Default Hostname</key>
        <string>store.data.rug.nl</string>
 
        <!-- iRODS port settings -->
        <key>Port Configurable</key>
        <false/>
        <key>Default Port</key>
        <string>1247</string>
 
        <!-- Default path to open -->
        <key>Default Path</key>
        <string>/rug/home</string>
 
        <!-- The zone of the iRODS server to connect to.  For backward -->
        <!-- compatibility, a root resource can be specified by appending -->
        <!-- ":<resource>" to the zone.  The specified resource is only -->
        <!-- used when uploading files.  Prefer setting "Destination -->
        <!-- Resource" under the "Properties" section. -->
        <key>Region</key>
        <string>rug</string>
 
        <!-- The authentication scheme used to establish a connection to -->
        <!-- an iRODS server.  Must be set to "native" or "pam_password". -->
        <!-- "standard" is an alias for "native". -->
        <key>Authorization</key>
        <string>pam_password</string>
 
        <!-- Advanced properties -->
        <key>Properties</key>
        <dict>
            <!-- The root resource to target when uploading files. -->
            <!-- DO NOT define this option unless needed. -->
            <!-- This option supersedes any resource defined by "Region". -->
            <key>Destination Resource</key>
            <string>rootResc</string>
 
            <!-- Controls whether deletion of an object permanently -->
            <!-- removes or moves it into the trash collection. -->
            <key>Delete Objects Permanently</key>
            <string>no</string>
 
            <!-- The size (in bytes) of a file that must be exceeded before -->
            <!-- using parallel transfer. -->
            <!-- The value must satisfy the range [1, 2^31-1]. -->
            <key>Parallel Transfer Threshold</key>
            <string>33554432</string>
 
            <!-- The number of iRODS connections used for parallel transfer -->
            <!-- of a single file.  Each transfer will use the specified -->
            <!-- number of iRODS connections. The value must satisfy the -->
            <!-- range [2, 10]. -->
            <key>Parallel Transfer Connections</key>
            <string>3</string>
 
            <!-- The buffer size (in bytes) used for parallel transfer of -->
            <!-- a single file. Applies to uploads and downloads.  The -->
            <!-- value must satisfy the range [1, 128MB]. -->
            <key>Parallel Transfer Buffer Size</key>
            <string>4194304</string>
 
            <!-- Secure communication options must be one of "CS_NEG_REQUIRE", -->
            <!-- "CS_NEG_DONT_CARE", or "CS_NEG_REFUSE". -->
            <!-- - CS_NEG_REQUIRE:   Demand TLS be used. -->
            <!-- - CS_NEG_DONT_CARE: Let the server decide if TLS is used. -->
            <!-- - CS_NEG_REFUSE:    Do not use TLS. -->
            <key>Client Server Negotiation</key>
            <string>CS_NEG_REQUIRE</string>
 
            <!-- TLS options, when enabled. -->
            <key>Encryption Algorithm</key>
            <string>AES-256-CBC</string>
            <key>Encryption Key Size</key>
            <string>32</string>
            <key>Encryption Salt Size</key>
            <string>8</string>
            <key>Encryption Hash Rounds</key>
            <string>16</string>
        </dict>
    </dict>
</plist>

RDMSsd.cyberduckprofile

<?xml version="1.0" encoding="UTF-8"?>
<!--
  ~ 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
  ~ (at your option) any later version.
  ~
  ~ This program is distributed in the hope that it will be useful,
  ~ but WITHOUT ANY WARRANTY; without even the implied warranty of
  ~ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  ~ GNU General Public License for more details.
  -->
 
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd">
<plist version="1.0">
    <dict>
        <!-- DO NOT CHANGE. This is the purpose of the profile-->
        <key>Protocol</key>
        <string>irods</string>
 
        <!-- Undocumented for CLI, the URI prefix, e.g., rug:// -->
        <key>Vendor</key>
        <string>sdrug</string>
 
        <!-- Name of the profile -->
        <key>Description</key>
        <string>RDMS (sdrugZone) 9.4.0+, iRODS 4.3.2+</string>
 
        <!-- Default name of bookmark -->
        <key>Default Nickname</key>
        <string>RDMS sdrugZone zone</string>
 
        <!-- iRODS hostname settings -->
        <key>Hostname Configurable</key>
        <false/>
        <key>Default Hostname</key>
        <string>store-sd.data.rug.nl</string>
 
        <!-- iRODS port settings -->
        <key>Port Configurable</key>
        <false/>
        <key>Default Port</key>
        <string>1247</string>
 
        <!-- Default path to open -->
        <key>Default Path</key>
        <string>/sdrugZone/home</string>
 
        <!-- The zone of the iRODS server to connect to.  For backward -->
        <!-- compatibility, a root resource can be specified by appending -->
        <!-- ":<resource>" to the zone.  The specified resource is only -->
        <!-- used when uploading files.  Prefer setting "Destination -->
        <!-- Resource" under the "Properties" section. -->
        <key>Region</key>
        <string>sdrugZone</string>
 
        <!-- The authentication scheme used to establish a connection to -->
        <!-- an iRODS server.  Must be set to "native" or "pam_password". -->
        <!-- "standard" is an alias for "native". -->
        <key>Authorization</key>
        <string>pam_password</string>
 
        <!-- Advanced properties -->
        <key>Properties</key>
        <dict>
            <!-- The root resource to target when uploading files. -->
            <!-- DO NOT define this option unless needed. -->
            <!-- This option supersedes any resource defined by "Region". -->
            <key>Destination Resource</key>
            <string>rootResc</string>
 
            <!-- Controls whether deletion of an object permanently -->
            <!-- removes or moves it into the trash collection. -->
            <key>Delete Objects Permanently</key>
            <string>no</string>
 
            <!-- The size (in bytes) of a file that must be exceeded before -->
            <!-- using parallel transfer. -->
            <!-- The value must satisfy the range [1, 2^31-1]. -->
            <key>Parallel Transfer Threshold</key>
            <string>33554432</string>
 
            <!-- The number of iRODS connections used for parallel transfer -->
            <!-- of a single file.  Each transfer will use the specified -->
            <!-- number of iRODS connections. The value must satisfy the -->
            <!-- range [2, 10]. -->
            <key>Parallel Transfer Connections</key>
            <string>3</string>
 
            <!-- The buffer size (in bytes) used for parallel transfer of -->
            <!-- a single file. Applies to uploads and downloads.  The -->
            <!-- value must satisfy the range [1, 128MB]. -->
            <key>Parallel Transfer Buffer Size</key>
            <string>4194304</string>
 
            <!-- Secure communication options must be one of "CS_NEG_REQUIRE", -->
            <!-- "CS_NEG_DONT_CARE", or "CS_NEG_REFUSE". -->
            <!-- - CS_NEG_REQUIRE:   Demand TLS be used. -->
            <!-- - CS_NEG_DONT_CARE: Let the server decide if TLS is used. -->
            <!-- - CS_NEG_REFUSE:    Do not use TLS. -->
            <key>Client Server Negotiation</key>
            <string>CS_NEG_REQUIRE</string>
 
            <!-- TLS options, when enabled. -->
            <key>Encryption Algorithm</key>
            <string>AES-256-CBC</string>
            <key>Encryption Key Size</key>
            <string>32</string>
            <key>Encryption Salt Size</key>
            <string>8</string>
            <key>Encryption Hash Rounds</key>
            <string>16</string>
        </dict>
    </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 at /rug/home/<username>@rug.nl, while Team Drives or your available Projects are located under /rug/home/<Team_Name> and /rug/home/Projects/<Project_Name>, respectively.

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.

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 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.

Finally, if you click the red box shown above, you will be given three options for 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 on what is going to be changed. Please also keep in mind that Cyberduck's synchronization feature 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 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.

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 to 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.

Furthermore, be sure that you disable the option for segmented downloads as this can introduce issues with your downloads.

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.