source: trunk/projects/ForwardCronJob/README.TXT @ 7726

Revision 7726, 1.6 KB checked in by ealexand, 9 years ago (diff)

This readme should explain the configuration of the cron job on open.microscopy.wisc.edu. CreateThumbnail.java and publish are also documented in further detail within their comments.

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1# README.TXT
2# Forward cron job
3
4This cron job takes .tiffs generated by WiscScan and uploads them to the UW-Forward database. It resides on the open.microscopy.wisc.edu machine. Specifically, the workflow looks like this:
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6    1. Scientists gather data, check the "Share with Forward" checkbox in the metadata dialog box.
7    2. This creates a METS companion file, which is copied to the users /data/username directory on open.microscopy.wisc.edu, along with the .ome.tiff files.
8    3. The cron job contained in the file "publish" runs hourly. When it detects new files in the /data directory, it does two things:
9        - Create a thumbnail for each dataset by running "CreateThumbnail.java"
10        - Copy the thumbnail and the METS companion file into /var/www/forward/adds directory
11    4. Forward queries the /var/www/forward/adds directory and links the files there to its website.
12   
13A couple of notes on setting this up properly. First, CreateThumbnail.java needs to be compiled with loci_tools.jar (found here: http://www.loci.wisc.edu/software/bio-formats). This file, along with /bftools (also on that same website) and the log4j.properties file should all be stored in the same directory as the publish script and CreateThumbnail.java. CreateThumbnail.java can then be compiled by running:
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15    javac -cp loci_tools.jar CreateThumbnail.java
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17After that, the publish script (which calls the Java program) should run correctly. To make it a cron job, it has been sym-linked to the /etc/cron.hourly/ directory.
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19For more information, see http://loci.wisc.edu/wiscscan/uw-forward-collaboration
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