[Resending (again) as GMail keeps mangling my email address… sorry for triple posting...]
Hi Björn, > Yes it is, but you need the :dev version, DOH, I should have known… > Can you explain what you delete? I do really support this idea as we are > also developing cheminformatics or imaging flavours. Currently I think I have just removed the datatypes. I haven’t removed anything else as I didn’t know how many, if any, were tightly coupled as the upload tool is. > >>>> Alternatively, does anyone have an automated process to delete >>>> unwanted tools that we could run immediately after cloning the >>>> main Galaxy repo? > > I don't think so you are pioneering here! But I think the gain of this > step is currently not much, isn't it? What are your concerns? Not really concerns, I just would like to remove as much unneeded code as possible. I have removed all (most) of the default datatypes shipped with Galaxy as many of the file extensions conflict with extension I want to use. Since the tools are most likely broken without the correct datatypes available my feeling is that these tools simply provide added points of failure and/or additional attack vectors for hackers. I have been dealing with some brute-force attacks on our Wordpress installation the past few weeks that has taught me that any unused code, regardless of how innocuous it seems, simply provides avenues of attack. > Yes it is, actually you need to have the upload tool, otherwise many > things do not work. > I would like to go with a)! I think you are correct; modifying the current upload tool is the way to go. A plugin mechanism for post-processing uploaded files sounds like a great idea! Cheers, Keith > > That is put big #if #else conditions in the JS and Galaxy code to > display genomic-specific content ... we could have a galaxy.ini config > to trigger this #if. > > I do think we have a good chance to get this accepted. > > Second step, and this will take for careful thoughts, is a plugin > mechanism for post-upload modifications. > The currently upload tool has some kind of these functionality, for > example the "Space-To-Tab" converter. Ideally exposing tools (even from > the TS)? > > >>>> I was hoping the "Downgrade upload tool" >>>> thread from a few weeks ago was going to help, but unfortunately >>>> for me (and good for the user) they found a solution that didn't >>>> involve installing a new upload tool. > > Let's try to stay as upstream as possible. upload.xml is so tightly > integrated in Galaxy that it is better to get code upstream I assume. > And I know Galaxy devs like the idea of being less genomic centric and > more a general framework. It's just that no one had time for this until > know. > >>>> However, could I follow the approach suggested in that thread? >>>> I.E. go back in time and find an old upload.[py | xml] and use >>>> that as a starting point for my own custom upload tool? How far >>>> back in time would I have to go to find an upload.py that was a >>>> standalone tool? > > I think this will cause more trouble ... :( > Let me know what you decide I will try to help you as much as I can. > > Cheers, > Bjoern > >>>> Cheers, Keith >>>> >>>> ------------------------------ Research Associate Department of >>>> Computer Science Vassar College Poughkeepsie, NY >>>> >>>> >>>> >>>> ___________________________________________________________ >>>> 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: >>>> https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> >>>> >>>> To search Galaxy mailing lists use the unified search at: >>>> http://galaxyproject.org/search/mailinglists/ >>>> <http://galaxyproject.org/search/mailinglists/> >>>> >> >> ------------------------------ Research Associate Department of >> Computer Science Vassar College Poughkeepsie, NY >> ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY > On Apr 4, 2016, at 7:01 PM, Suderman Keith <keithsuder...@gmail.com> wrote: > > Hi Björn, > >> Yes it is, but you need the :dev version, > > DOH, I should have known… > >> Can you explain what you delete? I do really support this idea as we are >> also developing cheminformatics or imaging flavours. > > Currently I think I have just removed the datatypes. I haven’t removed > anything else as I didn’t know how many, if any, were tightly coupled as the > upload tool is. > >> >>>>> Alternatively, does anyone have an automated process to delete >>>>> unwanted tools that we could run immediately after cloning the >>>>> main Galaxy repo? >> >> I don't think so you are pioneering here! But I think the gain of this >> step is currently not much, isn't it? What are your concerns? > > Not really concerns, I just would like to remove as much unneeded code as > possible. I have removed all (most) of the default datatypes shipped with > Galaxy as many of the file extensions conflict with extension I want to use. > Since the tools are most likely broken without the correct datatypes > available my feeling is that these tools simply provide added points of > failure and/or additional attack vectors for hackers. I have been dealing > with some brute-force attacks on our Wordpress installation the past few > weeks that has taught me that any unused code, regardless of how innocuous it > seems, simply provides avenues of attack. > >> Yes it is, actually you need to have the upload tool, otherwise many >> things do not work. >> I would like to go with a)! > > I think you are correct; modifying the current upload tool is the way to go. > A plugin mechanism for post-processing uploaded files sounds like a great > idea! > > Cheers, > Keith > >> >> That is put big #if #else conditions in the JS and Galaxy code to >> display genomic-specific content ... we could have a galaxy.ini config >> to trigger this #if. >> >> I do think we have a good chance to get this accepted. >> >> Second step, and this will take for careful thoughts, is a plugin >> mechanism for post-upload modifications. >> The currently upload tool has some kind of these functionality, for >> example the "Space-To-Tab" converter. Ideally exposing tools (even from >> the TS)? >> >> >>>>> I was hoping the "Downgrade upload tool" >>>>> thread from a few weeks ago was going to help, but unfortunately >>>>> for me (and good for the user) they found a solution that didn't >>>>> involve installing a new upload tool. >> >> Let's try to stay as upstream as possible. upload.xml is so tightly >> integrated in Galaxy that it is better to get code upstream I assume. >> And I know Galaxy devs like the idea of being less genomic centric and >> more a general framework. It's just that no one had time for this until >> know. >> >>>>> However, could I follow the approach suggested in that thread? >>>>> I.E. go back in time and find an old upload.[py | xml] and use >>>>> that as a starting point for my own custom upload tool? How far >>>>> back in time would I have to go to find an upload.py that was a >>>>> standalone tool? >> >> I think this will cause more trouble ... :( >> Let me know what you decide I will try to help you as much as I can. >> >> Cheers, >> Bjoern >> >>>>> Cheers, Keith >>>>> >>>>> ------------------------------ Research Associate Department of >>>>> Computer Science Vassar College Poughkeepsie, NY >>>>> >>>>> >>>>> >>>>> ___________________________________________________________ >>>>> 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: >>>>> https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/> >>>>> >>>>> To search Galaxy mailing lists use the unified search at: >>>>> http://galaxyproject.org/search/mailinglists/ >>>>> <http://galaxyproject.org/search/mailinglists/> >>>>> >>> >>> ------------------------------ Research Associate Department of >>> Computer Science Vassar College Poughkeepsie, NY >>> > > ------------------------------ > Research Associate > Department of Computer Science > Vassar College > Poughkeepsie, NY ------------------------------ Research Associate Department of Computer Science Vassar College Poughkeepsie, NY
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