[galaxy-dev] User information when creating a new user
Hi, when a new user creates a new account they only need an email address and password. This can be quite tricky to identify the user/demographics etc at a alter point. Is there a form that a user may complete where he could add optional data such as name, institution, address etc ? There is a table (user_address) that stores this information just not sure how/if it's populated Thanks Neil ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Default value for data_column not working?
Hmm So my understanding of the way Galaxy sort of iteratively builds up tool parameters is that each time there is a state update it validates all of the old state (this is where the red errors come from) and then generates the new state - but it never validates the new state before re-rendering the form. At the beginning the whole state is "new" and this is why you don't get the red warning initially for the column not existing but you do upon subsequent form re-renders. The easiest way to demonstrate this behavior is take an empty history and click on the concatenate datasets tool. There are no warning initially even though the data parameter is empty and invalid - but if you click to "Add New Dataset" to the tool - it re-renders and you get a warning on the first data input but not on the new one. Same thing happens to the second input if you add another dataset to the repeat. I do not know why the initial state is not validated, but the following quick patch forces that new state to be validated if you want this behavior. It implements the red warning you were hoping for (at least on the initial rendering of the tool). A more complete patch might seek to validate all new state - or re-validate everything after state has been populated. https://gist.github.com/jmchilton/72767b794445fae63426 Anyone aware of pitfalls of enabling this behavior? Anyone besides Peter feel it is an issue that should be addressed? -John On Tue, May 13, 2014 at 6:16 AM, Peter Cock wrote: > Thanks John, > > For now I am setting both the value and default_value tags, e.g. > https://github.com/peterjc/galaxy_blast/blob/master/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml > > However, in usability testing I have found a related problem/issue. > In this tool I ask for several columns, including one which defaults > to column 25. Provided the most recent tabular file in the history > has this many (or more) columns, everything is fine. > > The problem is that if the most recent tabular file has less columns > (e.g. 12), then the default value cannot be used - thus it is *silently* > replaced with 1. > > The same problem of the column parameters being changed to > column one can happen with switching the input file too. > > Once the user then switches to an appropriate tabular input file > (which does have enough columns), but the column defaults are > not reapplied, so column one gets used - and the output is wrong :( > > However, if I manually change a column option (e.g. to 24), then > switch to an input file with less columns, rather than a *silent* > substitution, although column one is picked, there is a nice red > warning: > > "An invalid option was selected, please verify " > > I think the simplest fix would be to reapply the defaults everytime > the associated input file is changed - but this might upset anyone > who had for whatever reason manually picked different columns. > > Can we have this red warning when the default value is not > possible and column one is substituted instead? > > Thanks, > > Peter > > P.S. Should this get a new Trello issue, or is the old one enough? > https://trello.com/c/6ugfcLgI/435-507-default-value-for-data-column-not-working-in-tool-xml > > On Mon, May 12, 2014 at 6:07 PM, John Chilton wrote: >> Hey Peter, >> >> I opened a pull request to allow the use of the value attribute and >> to allow column numbers to be prefixed by c. I cannot see any problem >> with either change and I have added some unit tests. Hopefully, this >> makes things more intuitive. >> >> https://bitbucket.org/galaxy/galaxy-central/pull-request/389/small-column-parameter-enhancements/diff >> >> Thanks, >> -John ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] backtrace from set_dataset_sizes.py
python scripts/set_dataset_sizes.py Loading Galaxy model... Processing 134520 datasets... Completed 0% Traceback (most recent call last): File "scripts/set_dataset_sizes.py", line 43, in dataset.set_total_size() File "lib/galaxy/model/__init__.py", line 1257, in set_total_size if self.object_store.exists(self, extra_dir=self._extra_files_path or "dataset_%d_files" % self.id, dir_only=True): AttributeError: 'NoneType' object has no attribute ‘exists' I’m seeing some odd sizes in galaxy, so I thought I’d attempt to re-initialize them. Is this expected to work? Brad -- Bradley W. Langhorst, Ph.D. Applications and Product Development Scientist ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Default value for data_column not working?
Thanks John, For now I am setting both the value and default_value tags, e.g. https://github.com/peterjc/galaxy_blast/blob/master/tools/blastxml_to_top_descr/blastxml_to_top_descr.xml However, in usability testing I have found a related problem/issue. In this tool I ask for several columns, including one which defaults to column 25. Provided the most recent tabular file in the history has this many (or more) columns, everything is fine. The problem is that if the most recent tabular file has less columns (e.g. 12), then the default value cannot be used - thus it is *silently* replaced with 1. The same problem of the column parameters being changed to column one can happen with switching the input file too. Once the user then switches to an appropriate tabular input file (which does have enough columns), but the column defaults are not reapplied, so column one gets used - and the output is wrong :( However, if I manually change a column option (e.g. to 24), then switch to an input file with less columns, rather than a *silent* substitution, although column one is picked, there is a nice red warning: "An invalid option was selected, please verify " I think the simplest fix would be to reapply the defaults everytime the associated input file is changed - but this might upset anyone who had for whatever reason manually picked different columns. Can we have this red warning when the default value is not possible and column one is substituted instead? Thanks, Peter P.S. Should this get a new Trello issue, or is the old one enough? https://trello.com/c/6ugfcLgI/435-507-default-value-for-data-column-not-working-in-tool-xml On Mon, May 12, 2014 at 6:07 PM, John Chilton wrote: > Hey Peter, > > I opened a pull request to allow the use of the value attribute and > to allow column numbers to be prefixed by c. I cannot see any problem > with either change and I have added some unit tests. Hopefully, this > makes things more intuitive. > > https://bitbucket.org/galaxy/galaxy-central/pull-request/389/small-column-parameter-enhancements/diff > > Thanks, > -John ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Keeping a tool from running multiple times at once
Peter I am not using a cluster, I am on a big computer with a lot of RAM. Plus I wouldn't know how to configure this, but thank you anyway ! Björn I didn't know about this file, but it seems really useful for what I'm willing to do. I don't totally understand what I should put in it yet, but I'm going to collect some informations about it to see if I can figure it out by myself before I decide if I have to bother you again. Thank you ! Guillaume 2014-05-13 12:16 GMT+02:00 Björn Grüning : > Hi Guillaume, > > you can set a limit for "concurrent_jobs" in job_conf.xml file. Please > have a look at the job_conf.xml.sample_advanced file for more information. > > Cheers, > Bjoern > > Am 13.05.2014 12:11, schrieb Guillaume Penderia: > >> Hi, >> >> I am currently working on a workflow with some custom tools, and one of >> these tools has to create very big temporary files (like 45Go big). >> As this workflow will be used on a lot of file at the same time, I have to >> keep it from running more than once or twice at the same time (the other >> execution would wait in the queue). If I don't, I'm afraid that some >> memory >> lack or something could cause all the executions to fail and stop. >> >> The problem is : I can't find if it's possible to do that, and if it is, >> how do I do it. >> >> Anyone has an idea please ? >> >> >> >> ___ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> >> ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Keeping a tool from running multiple times at once
Hi Guillaume, you can set a limit for "concurrent_jobs" in job_conf.xml file. Please have a look at the job_conf.xml.sample_advanced file for more information. Cheers, Bjoern Am 13.05.2014 12:11, schrieb Guillaume Penderia: Hi, I am currently working on a workflow with some custom tools, and one of these tools has to create very big temporary files (like 45Go big). As this workflow will be used on a lot of file at the same time, I have to keep it from running more than once or twice at the same time (the other execution would wait in the queue). If I don't, I'm afraid that some memory lack or something could cause all the executions to fail and stop. The problem is : I can't find if it's possible to do that, and if it is, how do I do it. Anyone has an idea please ? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Keeping a tool from running multiple times at once
On Tue, May 13, 2014 at 11:11 AM, Guillaume Penderia wrote: > Hi, > > I am currently working on a workflow with some custom tools, and one of > these tools has to create very big temporary files (like 45Go big). > As this workflow will be used on a lot of file at the same time, I have to > keep it from running more than once or twice at the same time (the other > execution would wait in the queue). If I don't, I'm afraid that some memory > lack or something could cause all the executions to fail and stop. > > The problem is : I can't find if it's possible to do that, and if it is, how > do I do it. > > Anyone has an idea please ? If you are using a cluster, one idea would be to setup a dedicated queue for these big jobs, configured to ensure only one runs at a time. Or at least, only one per cluster node. 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Keeping a tool from running multiple times at once
Hi, I am currently working on a workflow with some custom tools, and one of these tools has to create very big temporary files (like 45Go big). As this workflow will be used on a lot of file at the same time, I have to keep it from running more than once or twice at the same time (the other execution would wait in the queue). If I don't, I'm afraid that some memory lack or something could cause all the executions to fail and stop. The problem is : I can't find if it's possible to do that, and if it is, how do I do it. Anyone has an idea please ? ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
