Hi Greg, I did not get any answer unfortunately. I still do have errors when running the functional tests and I do not know how the tool shed will solve the problem as Nate replied to a related email regarding functional test failures. As far as I am aware, the most used tool for comparing the test outputs is 'diff'. It is perfectly fine when comparing text file but there are plenty of tools that produce PDF files, and as you mention they differ a lot even when generated under identical circumstances. However, to temporarily solve these differences, I've generated manually these files using the export GALAXY_TEST_SAVE=/data_ls/galaxy/test-data ran the test, visually compared the files and copied them back to test-data/ directory. Not very elegant and time consuming. Anyone with better solution? Cheers, Anne. On 26 Mar 2012, at 08:27, Greg Edwards wrote:

Hi Anne,

Just wondering if you got any response to your question, I'm interested to know the answer myself.

I'm not a PDF expert, but have done some work over the years with PDFs, PostScript, fonts etc. Even a small thing like the date/time generated in the PDF could make a diff fail, or the encoding of the system info it was generated on. Font library info gets included that can differ across systems. Plus diff thinks there is binary data in the PDF, which there can be, so that will cause diff to have hiccups.

I printed two identical PDF's, just a few chars, on my Mac and they differ a lot, even though created a few seconds apart under identical circumstances.

I don;t think 'diff' is much use to do a comparison in the functional tests, I'm surprised that they use that. Unless Galaxy has a cut down, simplified PDF generator that doesn;t encode any variable info, which I doubt.

Cheers, Greg E

On Tue, Mar 6, 2012 at 4:35 AM, Anne Pajon <Anne.Pajon@cancer.org.uk> wrote: Dear All,

I have noticed that some output files of functional tests are of type PDF. When comparing the one produced by the tool and the one stored in test-data/, they obviously differ even if they visually look identical.

Is there a better way to compare PDF files within Galaxy than using diff? If not, do you have experience or suggestion at solving these functional test failures?

Thanks a lot in advance. Kind regards, Anne. -- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cancer.org.uk | +44 (0)1223 404 334

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-- Anne Pajon, Ph.D. Cancer Research UK - Cambridge Research Institute Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE anne.pajon@cancer.org.uk | +44 (0)1223 404 334 NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above-named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered in England and Wales Company Registered Number: 4325234. Registered Charity Number: 1089464 and Scotland SC041666 Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD.