Re: [galaxy-dev] How to show alert message to user when running a tool in galaxy
On Apr 4, 2013, at 9:41 AM, BingXin Lu wrote: Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I have not found out an efficient way to implement this in galaxy. I am wondering if it is possible to give some warning message to users when running a tool in galaxy and how to do it if it is feasible. I implemented the tool with an xml file and a python file. I am wondering calling javascript from the python code to give user error information. But it seems infeasible and I do not know where to start. Hi Bingxin, The simplest method would be to output the messages from your tool. For a warning message that does not cause the tool to fail, write the messages to stdout. If the warning conditions should cause the tool to fail, write the messages to stderr. --nate Do you have any ideas? Thank you very much! Best regards, --Bingxin ___ 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] How to show alert message to user when running a tool in galaxy
I will try this method. Thank you very much! 2013/4/8 Nate Coraor n...@bx.psu.edu On Apr 4, 2013, at 9:41 AM, BingXin Lu wrote: Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I have not found out an efficient way to implement this in galaxy. I am wondering if it is possible to give some warning message to users when running a tool in galaxy and how to do it if it is feasible. I implemented the tool with an xml file and a python file. I am wondering calling javascript from the python code to give user error information. But it seems infeasible and I do not know where to start. Hi Bingxin, The simplest method would be to output the messages from your tool. For a warning message that does not cause the tool to fail, write the messages to stdout. If the warning conditions should cause the tool to fail, write the messages to stderr. --nate Do you have any ideas? Thank you very much! Best regards, --Bingxin ___ 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] How to show alert message to user when running a tool in galaxy
On Thu, Apr 4, 2013 at 2:51 PM, BingXin Lu soulsop...@gmail.com wrote: Dear all, I have added a tool in galaxy. After clicking 'Execute', this tool will query an external database for some information to ensure that there are no conflict records in the database. So sometimes an alert message should be sent to user if there are wrong records in the database. But I have not found out an efficient way to implement this in galaxy. I am wondering if it is possible to give some warning message to users when running a tool in galaxy and how to do it if it is feasible. I implemented the tool with an xml file and a python file. I am wondering calling javascript from the python code to give user error information. But it seems infeasible and I do not know where to start. Do you have any ideas? Thank you very much! Best regards, --Bingxin Can you treat this as an error? If so just write the message to stderr, and Galaxy will show this to the user as the 'info' text for the failed history entry (and also available via the stderr link via the 'i' icon). 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/
Re: [galaxy-dev] How to show alert message to user when running a tool in galaxy
On Thu, Apr 4, 2013 at 3:23 PM, BingXin Lu soulsop...@gmail.com wrote: Thanks a lot, it is a solution. However, I think it is more user-friendly to give user instant prompt when detecting conflict in the database, so that user can decide to override current record in the database or keep current record and stop running the tool again. I'm not aware of anything like that being done via the param's validator tag... but that is the appropriate place for any checks on a parameter before the execute button is pressed. Peter P.S. Don't forget to include the mailing list in replies. ___ 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/
