This is a command-line Java application that you can use to efficiently upload your data into Mediaflux and make integrity checks. Installation instructions are available in the parent page

This client can

upload files in parallel (--nb-workers). There is no magic in this, it will only go faster if there is sufficient network capacity. Therefore, please don't use more than 4 upload threads. You may even find that if the network is heavily congested, 4 threads is no faster than 1. You may have to experiment a little to find the optimum.
compute checksums for additional validation (see below)
write a log file of the upload
generate and email a summary of the upload (including successful and failed uploads, and the number of zero-sized files it encountered)
run in daemon mode (in the background) so it keeps uploading new data to Mediaflux as it arrives in your local file system
Please see all command-line arguments with the --help switch

Here are all the details for the command-line arguments to this client.

Pre-existing files

The client checks whether files already exist in Mediaflux or not. If they do exist it will skip the upload. The checks it uses are:

File path/name exists and is the same
File size is the same
If checksums are enabled, the checksum is the same

If any of these fail, the file does not pre-exist and will be re-uploaded. In the case that the path/name is the same, but the source file has changed content, it will be uploaded to the pre-existing asset in Mediaflux as a new version.

Checksums

Checksums (a unique number computed from the contents of a file) are an important data integrity mechanism. The Mediaflux server computes a checksum for each file it receives. The upload client can compute checksums from the source data on the client side and compare with the checksum computed by the server when it receives the file. If the checksums match, we can be very confident that the file uploaded correctly. Many other clients for other protocols (e.g. sFTP and SMB) do not do this.

By default, checksums are not enabled (because computing checksums slows down the upload process). However, it is strongly recommended that you enable these during the upload or run the checker client unimelb-mf-check with checksums to check the upload afterwards.

Case 1 - Files DO NOT pre-exist on Mediaflux

When you enable checksums, and the data DO NOT already exist on the server, the client will compute the check sum as part of the upload process. When Mediaflux creates the asset, it will also compute the checksum. These checksums will be compared.

Case 2 - Files DO pre-exist on Mediaflux

When you enable checksums, and the data DO already exist on the server (by path/name and size), then client will compute the check sum on the local file first and compare the checksum with that already stored in Mediaflux.

If the checksums differ, it will then proceed to re-upload the local file (following the process in Case 1. above) because it has changed and make a new asset version. Thus, overall 2 checksums are computed by the client and one by the server.

Examples

You will need to know where (the path) to locate your data in Mediaflux (the --dest argument of the command) and where to upload from (the last positional argument)

Example 1 - parallel upload with checksum check

Upload data with four worker threads and turn on checksums for upload integrity checking (recommended). As the location of the config files is not specified, the client will look for it in the .Arcitecta directory of your home directory.

unimelb-mf-upload --csum-check --nb-workers 4 --dest /projects/proj-myproject-1128.1.59/12Jan2018 /data/projects/punim0058

Example 2 - using a configuration file

Upload data with one worker thread and specify explicitly where the configuration file is.

unimelb-mf-upload --mf.config /Users/nebk/.Arcitecta/mflux.cfg  --dest /projects/proj-myproject-1128.1.59/12Jan2018 /data/projects/punim0058

The Configuration File might look like this:

host=mediaflux.researchsoftware.unimelb.edu.au
port=443
transport=https
token=phooP1Angohb2ooyahbiLiuwa6ahjuoKooViedaifooPhiqu1ookahXae7keichael4Shae2ael8ietit2phawucai0Aighifu6olah9OquahDei2aevae3keich8ain1OoLa4O

Scheduled uploads

If you have a location that should be uploaded on a regular schedule such as an instrument PC that saves data to a given directory on the local computer, you can schedule uploads with unimelb-mf-upload. It is best to request an upload token if you want to do this as the credential will be stored on the computer that is doing the uploads. Contact Research Computing Services to request a token.

Windows

In this example:

we will put the unimelb-mf-client files in the %HOMEPATH%\Documents directory
we will save logs to the %HOMEPATH%\Documents\logs directory
will will put the configuration file in the %HOMEPATH%\Documents directory

Download from the GitLab page, selecting the Windows 64bit release. Extract the zip file to %HOMEPATH%\Documents.

Create a Configuration File. In this case we are going to use a secure token. In our example, it will be stored in %HOMEPATH%\Documents\mflux.cfg.

host=mediaflux.researchsoftware.unimelb.edu.au
port=443
transport=https
token=phooP1Angohb2ooyahbiLiuwa6ahjuoKooViedaifooPhiqu1ookahXae7keichael4Shae2ael8ietit2phawucai0Aighifu6olah9OquahDei2aevae3keich8ain1OoLa4O

Create a batch file to perform the upload using Notepad. In our example, it will be stored in %HOMEPATH%\Documents\upload.bat:

%HOMEPATH%\Documents\unimelb-mf-clients-0.7.7\bin\windows\unimelb-mf-upload --mf.config %HOMEPATH%\Documents\mflux.cfg --log-dir %HOMEPATH%\Documents\logs --dest /projects/proj-demonstration-1128.4.15 %HOMEPATH%\Documents\data-to-upload

Schedule the upload using Windows Task Scheduler.

Click the start button and start typing Task Scheduler and select it from the Start Menu when it appears.
Click on the Task Scheduler Library, then right click on the space and choose Create Basic Task... from the menu.

Give your task a name and description, then click Next >
choose a start date and time and click Next >
choose Start a program and click Next >
click the Browse button and find the script you created above.
Click Next > and then check the Open the Properties dialog for this task when I click Finish box, then click Finish.
Under Security options, choose which user you would like the task to run under. You may wish to make it so the scheduled job will run even if the user is not logged in.

Linux

In this example:

we will put the unimelb-mf-client files in the ~/bin directory
we will save logs to the ~/logs directory
will will put the configuration file in the ~/.Arcitecta directory

Download from the GitLab page, selecting the Linux 64bit release. Extract the zip file to ~/bin.

Create a Configuration File. In this case we are going to use a secure token. In our example, it will be stored in ~/.Arcitecta/mflux.cfg.

host=mediaflux.researchsoftware.unimelb.edu.au
port=443
transport=https
token=phooP1Angohb2ooyahbiLiuwa6ahjuoKooViedaifooPhiqu1ookahXae7keichael4Shae2ael8ietit2phawucai0Aighifu6olah9OquahDei2aevae3keich8ain1OoLa4O

Create a shell script to perform the upload using the text editor of your choice. In our example, it will be stored in ~/bin/upload.sh:

#!/bin/bash
~/bin/unimelb-mf-clients-0.7.4/bin/unix/unimelb-mf-upload --mf.config ~/.Arcitecta/mflux.cfg --log-dir ~/logs --dest /projects/proj-demonstration-1128.4.15 ~/data-to-upload

On Linux there's typically two options for scheduling tasks: cron and systemd timers. In this example, we will use a cron job.

Edit the crontab file with the following command:

crontab -e

Create a new scheduled task at the end of the crontab file. To see documentation on the format, try the man 5 crontab command. In our example, we will run the command once per day at 1 am local time.

# To define the time you can provide concrete values for
# minute (m), hour (h), day of month (dom), month (mon),
# and day of week (dow) or use '*' in these fields (for 'any').
#
# For more information see the manual pages of crontab(5) and cron(8)
# 
# m h  dom mon dow   command
0 1 * * * $HOME/bin/upload.sh

Save the file, and your job will be scheduled.

crontab: installing new crontab

macOS

In this example:

we will put the unimelb-mf-clients in the ~/Applications folder
we will save logs to the ~/Documents/logs folder
we will put the configuration file in the ~/.Arcitecta folder

Download from the GitLab page, selecting the Mac 64bit release. Extract the tar.gz file by clicking on it. It will be extracted to a folder in your Downloads folder, so move it o the Applications folder.

Create a Configuration File. In this case we are going to use a secure token. In our example, it will be stored in ~/.Arcitecta/mflux.cfg.

host=mediaflux.researchsoftware.unimelb.edu.au
port=443
transport=https
token=phooP1Angohb2ooyahbiLiuwa6ahjuoKooViedaifooPhiqu1ookahXae7keichael4Shae2ael8ietit2phawucai0Aighifu6olah9OquahDei2aevae3keich8ain1OoLa4O

Create a shell script to perform the upload using the text editor of your choice. In our example, it will be stored in ~/bin/upload.sh:

#!/bin/bash
~/Applications/unimelb-mf-clients-0.7.4/bin/unix/unimelb-mf-upload --mf.config ~/.Arcitecta/mflux.cfg --log-dir ~/logs --dest /projects/proj-demonstration-1128.4.15 ~/data-to-upload

Edit the crontab file with the following command. By default the vim text editor will be used.

crontab -e # this will use the default text editor, usually vim

# if you would prefer to use the pico text editor, use the following command instead:
EDITOR=/usr/bin/pico crontab -e

Create a new scheduled task at the end of the crontab file. To see documentation on the format, try the man 5 crontab command. In our example, we will run the command once per day at 1 am local time.

# To define the time you can provide concrete values for
# minute (m), hour (h), day of month (dom), month (mon),
# and day of week (dow) or use '*' in these fields (for 'any').
#
# For more information see the manual pages of crontab(5) and cron(8)
# 
# m h  dom mon dow   command
0 1 * * * $HOME/bin/upload.sh

Save the file, and your job will be scheduled.

crontab: installing new crontab

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