Re: [galaxy-dev] Plotting tools - best output format? PDF, PNG, ... SVG!
On Thu, Apr 21, 2011 at 10:50 AM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 5:47 PM, Peter Cock wrote: On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 11:07 AM, Peter Cock wrote: Hi all, ...cut... How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? Yep, SVG support is pretty good nowadays especially in FireFox and Opera. Safari, IE and Chrome have only partial support, but for simple charts without 3D filters it works fine. I've added SVG as a datatype to my Galaxy and this works great. You won't need a plugin; in fact the old Adobe SVG plugin is depreciated already for a few years now and no longer compatible with recent browser versions. I looked at SVG about a year ago, and was pretty impressed. I did run into some issues, particularly with links, and opted to use PNG files in the end. Since then we've finally dropped IE6, so hopefully SVG would be safe now. Are your changes to add SVG as a datatype to Galaxy public? I'd like to suggest that be merged to the trunk. I simply added this line to my datatypes_conf.xml: datatype extension=svg type=galaxy.datatypes.images:Image mimetype=image/svg+xml/ I didn't make a sniffer as I don't have a use case for users uploading SVGs, so I didn't have to create a Python class and SVG is just another instance of galaxy.datatypes.images:Image from a plain vanilla Galaxy. That makes sense if the sniffer is only used on upload. To make sure the client displays the SVG you may have to add the SVG mimetype to your web server's config too. Where this is defined may differ per linux distro. I use apache as a proxy and had to add image/svg+xml svg svgz to /etc/mime.types. Thanks for the details - it looks simple enough to add here too. If/when any SVG producing tools are added to Galaxy or the Galaxy Tool Shed, then it would be nice to have this done in the main repository. The nice benefit of SVG in addition to not needing a plugin is that the image can scale with the surrounding text if you zoom in your browser (without loosing resolution). The disadvantage is that although my users know what a PDF file is and can process them for posters/manuscripts, most of them never heard of SVG and get stuck when it doesn't import into PowerPoint et al. :( Do they cope with PDF? Well, they know how to view and print one :). Importing them directly into PowerPoint and Word is just as problematic though, so that usually involves opening the PDF in a different program and copy/paste or exporting to another format. Still a hassle, but they manage... Getting a PDF into PowerPoint or Word is easy on a Mac ;) But yes, point taken - even though a PDF is easier to work with than an SVG (or a postscript file), it can still be a hassle. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Plotting tools - best output format? PDF, PNG, ...
Hi all, I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications. However, at least on my OS/Browser, Galaxy does not show the PDF files in situ, the eye button acts like a download link. Is this a bug? If I switch to making a PNG file, then clicking on the eye button shows the image directly in the center panel (nice), but PNG is not a great format for detailed figures or printing. Looking over the tools which come with Galaxy under tools/plotting/*.xml all use PDF or PNG. How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Plotting tools - best output format? PDF, PNG, ...
On Wed, Apr 20, 2011 at 10:07 AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, I'm working on a simple plotting tool, and currently I am using PDF output since this is vector based (so it can be rescaled without loss of quality) and can be edited easily enough for use in publications. However, at least on my OS/Browser, Galaxy does not show the PDF files in situ, the eye button acts like a download link. Is this a bug? Looks like a Firefox issue/setting - false alarm: On our local Galaxy, with a PDF entry in the history, and as a control http://nar.oxfordjournals.org/content/39/7/2492.full.pdf+html which should show a PDF embedded on the left: Windows XP, Internet Explorer 7.05730.13 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Windows XP, Chrome 10.0.648.204 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Windows XP, Firefox 3.6.13 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. Linux CentOS, Firefox 3.6.13 - NAR downloads PDF, shows left pane empty, usable. - Clicking on the eye, downloads the PDF, usable. - Clicking on the disk, saves the PDF, good. Mac OS X 10.6, Firefox 4.0 - NAR downloads PDF, shows left pane empty, usable. - Clicking on the eye, downloads the PDF, usable. - Clicking on the disk, saves the PDF, good. Mac OS X 10.6, Safari 5.0.5 - NAR shows PDF on left, good - Clicking on the eye, shows the PDF in the central panel, good. - Clicking on the disk, saves the PDF, good. So it looks like Firefox can (probably dependent on the user's settings) download PDF files rather than show them in situ. That's fine, and not specific to Galaxy. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Plotting tools - best output format? PDF, PNG, ... SVG!
On Wed, Apr 20, 2011 at 4:30 PM, Pieter Neerincx pieter.neeri...@gmail.com wrote: Hi Peter, On Apr 20, 2011, at 11:07 AM, Peter Cock wrote: Hi all, ...cut... How about SVG? Don't most of the mainline browsers have reasonably good SVG support built in (possibly via a plugin)? Yep, SVG support is pretty good nowadays especially in FireFox and Opera. Safari, IE and Chrome have only partial support, but for simple charts without 3D filters it works fine. I've added SVG as a datatype to my Galaxy and this works great. You won't need a plugin; in fact the old Adobe SVG plugin is depreciated already for a few years now and no longer compatible with recent browser versions. I looked at SVG about a year ago, and was pretty impressed. I did run into some issues, particularly with links, and opted to use PNG files in the end. Since then we've finally dropped IE6, so hopefully SVG would be safe now. Are your changes to add SVG as a datatype to Galaxy public? I'd like to suggest that be merged to the trunk. The nice benefit of SVG in addition to not needing a plugin is that the image can scale with the surrounding text if you zoom in your browser (without loosing resolution). The disadvantage is that although my users know what a PDF file is and can process them for posters/manuscripts, most of them never heard of SVG and get stuck when it doesn't import into PowerPoint et al. :( Do they cope with PDF? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
