[galaxy-dev] Bug report: page within help
Hello, I found that it is possible for tool-xmls defined with page tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two pages): help page Helptext for page 1 /page page Helptext for page 2 /page /help But for it to work one has to fix the following: rev 13771:7a4d321c0e38 file lib/galaxy/tools/__init__.py expression starting at line 1439: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] The bracket is misplaced and the whole thing should instead be: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) for x in self.help_by_page ] One question: page is deprecated, does this mean there will be no multipage tools in the future? Or will there be (or is already?) an alternative system? Best, Philipp ___ 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] Bug report: page within help
Philipp, Pages are seriously deprecated -- do not use them. Many things will not work, they are not supported in workflows, the API, et cetera. They only still exist for backward compatibility with ANCIENT tools. Thanks, James -- jt On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel hans-philipp.brachvo...@student.uni-tuebingen.de wrote: Hello, I found that it is possible for tool-xmls defined with page tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two pages): help page Helptext for page 1 /page page Helptext for page 2 /page /help But for it to work one has to fix the following: rev 13771:7a4d321c0e38 file lib/galaxy/tools/__init__.py expression starting at line 1439: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] The bracket is misplaced and the whole thing should instead be: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) for x in self.help_by_page ] One question: page is deprecated, does this mean there will be no multipage tools in the future? Or will there be (or is already?) an alternative system? Best, Philipp ___ 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] Bug report: page within help
Hey James thanks for the feedback! But on the other hand I know of no alternative to creating an input form with several steps/pages/subforms, or is there? Our group really wants something like this to enhance the user friendliness for some tools with rather complicated input stages... actually I even added the functionality of going back a page into our galaxy version... Best, Philipp On 12 Aug 2014, at 14:05, James Taylor ja...@jamestaylor.org wrote: Philipp, Pages are seriously deprecated -- do not use them. Many things will not work, they are not supported in workflows, the API, et cetera. They only still exist for backward compatibility with ANCIENT tools. Thanks, James -- jt On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel hans-philipp.brachvo...@student.uni-tuebingen.de wrote: Hello, I found that it is possible for tool-xmls defined with page tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two pages): help page Helptext for page 1 /page page Helptext for page 2 /page /help But for it to work one has to fix the following: rev 13771:7a4d321c0e38 file lib/galaxy/tools/__init__.py expression starting at line 1439: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] The bracket is misplaced and the whole thing should instead be: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) for x in self.help_by_page ] One question: page is deprecated, does this mean there will be no multipage tools in the future? Or will there be (or is already?) an alternative system? Best, Philipp ___ 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] Bug report: page within help
I have applied your patch here (https://bitbucket.org/galaxy/galaxy-central/commits/19309418c86450b7f39691460eb430e100883cb4) and one correction to James' previous comment - multi-page tools actually do work through the API - this was required for multi-page tool testing via the API. -John On Tue, Aug 12, 2014 at 8:18 AM, Hans-Philipp Brachvogel hans-philipp.brachvo...@student.uni-tuebingen.de wrote: Hey James thanks for the feedback! But on the other hand I know of no alternative to creating an input form with several steps/pages/subforms, or is there? Our group really wants something like this to enhance the user friendliness for some tools with rather complicated input stages... actually I even added the functionality of going back a page into our galaxy version... Best, Philipp On 12 Aug 2014, at 14:05, James Taylor ja...@jamestaylor.org wrote: Philipp, Pages are seriously deprecated -- do not use them. Many things will not work, they are not supported in workflows, the API, et cetera. They only still exist for backward compatibility with ANCIENT tools. Thanks, James -- jt On Tue, Aug 12, 2014 at 4:59 AM, Hans-Philipp Brachvogel hans-philipp.brachvo...@student.uni-tuebingen.de wrote: Hello, I found that it is possible for tool-xmls defined with page tags to also have multipage helps, but this feature is not really documented and also does not work because of a tiny bug. You can have multipage helps by writing something like this (if your tool has two pages): help page Helptext for page 1 /page page Helptext for page 2 /page /help But for it to work one has to fix the following: rev 13771:7a4d321c0e38 file lib/galaxy/tools/__init__.py expression starting at line 1439: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] The bracket is misplaced and the whole thing should instead be: self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) for x in self.help_by_page ] One question: page is deprecated, does this mean there will be no multipage tools in the future? Or will there be (or is already?) an alternative system? Best, Philipp ___ 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/ ___ 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/
