LibSEDML: Sharing Simulation Experiments Activity
Status: Beta
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fbergmann
Activity for LibSEDML: Sharing Simulation Experiments
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Frank Bergmann committed [r253]
- added missing addxml / remove xml
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- fix an issue with retrieving elements from https
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- include oscli model in archive, to ensure it can be resolved
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- include oscli model in archive, to ensure it can be resolved
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- updated example
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investigate issue with cellml & ca
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This has now been resolved using a new version of the csim library ... the original archive is now working as well. Thanks David!
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- use new csim library, ensure that we always pass along uris
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- support display of l1v3 elements
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- improve support for L1v3, add validation
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Data generate evaluate minus with one child missing a 'minus'?
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Create larger size images in combine archive with results
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Sed-ML Webtools: max function not applied on DataGenerator
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Vanderpol omex does not give results
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Matthias König posted a comment on ticket #15
Thanks. This can be closed. On Wed, Oct 4, 2017 at 9:53 AM, Frank Bergmann fbergmann@users.sf.net wrote: In order to resolve the elements I take the full xml document and use an xpath navigator to resolve the individual elements. The xpath navigator will give you the corresponding DOM element. [tickets:#15] https://sourceforge.net/p/libsedml/tickets/15/ Vanderpol omex does not give results* Status: open Milestone: 1.0 Created: Wed Sep 27, 2017 12:58 PM UTC by Matthias König Last Updated: Fri Sep...
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Mass balance not conserved in parameter-scan-2d
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This can be closed. I included your changes in the L1V3 example and updated the SED-ML web tool figures in the spec. Thanks. On Wed, Oct 4, 2017 at 9:55 AM, Frank Bergmann fbergmann@users.sf.net wrote: I've deployed a new version that takes care of the regression. Thanks [tickets:#16] https://sourceforge.net/p/libsedml/tickets/16/ Mass balance not conserved in parameter-scan-2d* Status: open Milestone: 1.0 Created: Fri Sep 29, 2017 07:30 PM UTC by Matthias König Last Updated: Mon Oct 02, 2017 01:45...
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Thanks a lot. This solves the issue for me. Can be closed. I don't need PDF from the webcalls as long as I can create larger PNG. I created the spec images like you suggested via PDF export. Thanks for this. On Wed, Oct 4, 2017 at 9:54 AM, Frank Bergmann fbergmann@users.sf.net wrote: I've deployed a new version that saves images by default with a resolution of 800x600 ... additionally the web calls now take a width and height parameter that allows you to customize the static images. For PDFs i suggest...
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Is fixed and can be closed. Already updated the L1V3 spec with the image. Thanks.
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this has been resolved, the issue is that current versions of libSBML will not parse the max mathml ... for now the web tools use a custom version of libsbml
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- use special version of libsbml that does not use SBML Namespaces for parsing mathml
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- update libsbml to a newer version
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I've deployed a new version that takes care of the regression. Thanks
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I've deployed a new version that saves images by default with a resolution of 800x600 ... additionally the web calls now take a width and height parameter that allows you to customize the static images. For PDFs i suggest to use the manual export for now.
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In order to resolve the elements I take the full xml document and use an xpath navigator to resolve the individual elements. The xpath navigator will give you the corresponding DOM element.
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- update roadrunner
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- save images by default in higher resolution
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- allow to pass parameter to determine image size
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updated omex file labelling the plot, and adding relevant elements to the report
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works locally, maybe we ought to change the omex to make it more apparent where it goes wrong.
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Expected output attached for plot2D postprocessing.
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Sed-ML Webtools: max function not applied on DataGenerator
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just click on the hamburger menu to get the pdf export of an image
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You will get support for higher resultions of the png export, i will not implement a separate PDF export however, for the API ... that would require different libraries. That being said, you can download PDFs and SVGs right from the interactive version on the website ... that should be good enough for the spec
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Tellurium gives just the flatline (with some numerical errors), see figure attached. This worked at some point with the webtools.
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Mass balance not conserved in parameter-scan-2d
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Hi Frank, thanks for this. This is solved. I thought that something was wrong with the archive, but could not figure it out. Yes, currently I am doing some lazy heuristics for the xpath resolving instead of applying xpath on the XML :/ See https://github.com/sys-bio/tellurium/issues/114 But seems to work for 99% of all archives I encountered so far. The point I don't understand is how I get from the xpath my SBML SBase element. I can take the SBML XML, apply the xpath and get back some XML, for instance...
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Hi Frank, I would need the better image quality for the L1V3 specification figures of SED-ML webtools. Best would be if I could somehow get a PDF from the static images. I can include these than directly in the spec. The current pictures are only the low resolution PNG or the PDF created from the webpage by export via Javascript (but these do not look so nice than the static images). I mainly need some way to get PDF plots from a combine archive executed with SED-ML webtools. Best via webservice,...
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Hello Matthias, the issue is with the xpath expression in the model. It seems that tellurium is not using xpath at all, otherwise it would not find a species under the listOfParameters. When you replace the xpath expression like in the screenshot, then all is good
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Expected results are attached (ignore the line returning to zero, this is still a bug in tellurium)
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Vanderpol omex does not give results
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Yes, a parameter for the webservice would be perfect. Than I can get just the plots in high resolution.
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A parameter can be added that allows to specify the dimensions of the graphics. Currently that is 640x480. Unfortunately the parameter is currently not customizable, but that could be changed. I'll update the item when this is done. I hope to get to it on the weekend. As for the name of the folder ... i don't see a point of calling the plot webtools ... after all the web tools are not a simulator by itself, instead for ODEs it uses the sbw roadrunner, for stochastic simulations it uses currently...
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While debugging I found the soruce of the issue. In both cases the issue is with the csim.dll that unfortunately causes the web server process to crash. Interestingly, in the one the issue https://sourceforge.net/p/libsedml/tickets/14/ that matthias found, the crash occurs on the second call to the csim.dll and results in an access violation. So far I have not yet managed to build it successfully. This will have to wait on a newer version of the dll.
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This issue is a duplicate of https://sourceforge.net/p/libsedml/tickets/12/
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CellML combine archive simulates but does not export static images
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CellML combine archive simulates but does not export static images
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David Nickerson posted a comment on ticket #12
Using the archive available from https://models.physiomeproject.org/e/4c7 everything seems to be working fine - so either this issue is fixed or there is a problem with my original test archive :)
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Create larger size images in combine archive with results
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investigate issue with cellml & ca
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Show static image option does not show static image
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thanks
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SED-ML web tools not returning results
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Thanks!
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Everything working now. Thanks a lot. Can be closed. M
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Thanks a lot. This is working now. Can be closed.
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this was due to a library mismatched on the deployed server ... and has been fixed
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Thanks for letting me know, I've redeployed the application with the correct version of the compression library. It should just work now.
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- ensure correct version of zip library is used
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could you attach a file that reproduces the issue? thank you
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Show static image option does not show static image
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SED-ML web tools not returning results
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- updated ignore list
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- fix calculation of uniform range
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- store information about local parameters in u...
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Thanks for all the fixes. This makes it much easier for me to compare the outputs...
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outputReports not correct for RepeatedTask & not written in combine
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Models from Combine Archives are not used in WebTools
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outputStartTime not interpreted correctly in WebTools
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Indeed it is not resolved how tools ought to plot the different repeats, I hope a...
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Problem with SedDataGenerator::setMath
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support for the non-standard max symbol has been added.
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Normalized plot not generated (problems with max in DataGenerator)
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SEDML Web tools does not handle ComputeChange on Model
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compute change has been updated to look at more places for the corresponding val...
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- issue #2: fix path in brusselator.xml
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Samples/sed-ml file has hardcoded model source
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sorry about the delay, this has been fixed.
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- issue #2: fix path in kholodenko examples
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A fix has been committed and a new version of the webtools are deployed. thanks!
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- fixed invalid references in examples
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- issue #9: added support for n-ary plus / time...
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Data generate evaluate minus with one child missing a 'minus'?
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agreed! ... looking at that code it actually does seem as if someone just copied...
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Data generate evaluate minus with one child missing a 'minus'?
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- linecolor
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- added line and FillColor
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- first version of webtools with support for co...
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- don't display reports without any columns
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- capitalization change
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- add version information at bottom of screen,
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- added js / css files to project
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- major speedup in evaluate
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- don't assume that key and value have same size
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- add odd versions of min / max / sum /product
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- plot symbols if line has only one element
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- prevent roadrunner from resetting
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- add toggle between highcharts and zedgraph
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-improve display of reports / tooltips on highc...
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LibSEDML: Sharing Simulation Experiments released /SetupSedML-win32-1.23.exe
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