refresh_on_change is broken?
Hello, Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem? regards, Leandro
Hi everyone, Sorry to ping again, having the refresh_on_change functionality not working in Galaxy has us making tool forms in ways we really don't want to, no one needs to use refresh_on_change or am I the only one that finds it's broken? We've started to look at what Galaxy is trying to do, seems like you are using jQuery to bind a custom Javascript refresh_on_change function but when you look at that function it doesn't do any form reloading, maybe just the feature is unfinished? sincerely, Leandro On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida <softdev@leandrohermida.com> wrote:
Hello,
Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem?
regards, Leandro
Leandro, refresh_on_change is used quite a bit throughout the tool UI and appears to work fine both on a local instance and on the public instance. E.g. look at Tophat and change settings from 'Use Defaults' to 'Full Parameter List' -- the refresh_on_change works on reload the tool with more parameters. Some questions that should shed light on your issues: *Does the Tophat tool refresh on the main server? If not, this is probably a browser issue. *Are you seeing any errors in the Javascript console? *Can you be more specific about what problems you're seeing and whether you can reproduce with known tools? Thanks, J. On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote:
Hi everyone,
Sorry to ping again, having the refresh_on_change functionality not working in Galaxy has us making tool forms in ways we really don't want to,
no one needs to use refresh_on_change or am I the only one that finds it's broken? We've started to look at what Galaxy is trying to do, seems like you are using jQuery to bind a custom Javascript refresh_on_change function but when you look at that function it doesn't do any form reloading, maybe just the feature is unfinished?
sincerely, Leandro
On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida <softdev@leandrohermida.com> wrote:
Hello,
Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem?
regards, Leandro
___________________________________________________________ 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:
Dear Jeremy, On Tue, Mar 20, 2012 at 6:19 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Leandro,
refresh_on_change is used quite a bit throughout the tool UI and appears to work fine both on a local instance and on the public instance. E.g. look at Tophat and change settings from 'Use Defaults' to 'Full Parameter List' -- the refresh_on_change works on reload the tool with more parameters.
Maybe we don't understand the feature in the documentation, but this isn't the refresh_on_change functionality. In the Tophat tool XML there are no refresh_on_change="true" attributes, you are talking about a conditional tag which when changing will refresh the page in order to expose different parts of a form depending on then value chosen, this is a different use case. The feature we thought exists from the wiki docs is a utility refresh_on_change="true" attribute that you can put on any input param tag which will cause the page to refresh with the changed state when you change the param. It's supposed to replace the deprecated pages tags. Once we started needing to make more complex form logic you realize that this is not just very useful but necessary. Here's one example: <inputs> <param type="data" name="dataset" refresh_on_change="true" label="Select a file from you history" /> <param type="select" multiple="true" name="dataset_values" dynamic_options="get_options_from_file(dataset.file_name)" /> </inputs> If the user changes their selection of data from their history it should refresh the page and call the dynamic options again to load the other select menu with the choices from the new file. Currently you have to do this with repeat or pages tags which is really cumbersome for the user in the UI or doesn't allow workflowing, respectively. Does this feature I describe to replace the deprecated pages tags not exist or just isn't fully implemented yet? regards, Leandro
Some questions that should shed light on your issues: *Does the Tophat tool refresh on the main server? If not, this is probably a browser issue. *Are you seeing any errors in the Javascript console? *Can you be more specific about what problems you're seeing and whether you can reproduce with known tools?
Thanks, J.
On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote:
Hi everyone,
Sorry to ping again, having the refresh_on_change functionality not working in Galaxy has us making tool forms in ways we really don't want to,
no one needs to use refresh_on_change or am I the only one that finds it's broken? We've started to look at what Galaxy is trying to do, seems like you are using jQuery to bind a custom Javascript refresh_on_change function but when you look at that function it doesn't do any form reloading, maybe just the feature is unfinished?
sincerely, Leandro
On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida <softdev@leandrohermida.com> wrote:
Hello,
Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem?
regards, Leandro
___________________________________________________________ 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:
Maybe we don't understand the feature in the documentation, but this isn't the refresh_on_change functionality. In the Tophat tool XML there are no refresh_on_change="true" attributes, you are talking about a conditional tag which when changing will refresh the page in order to expose different parts of a form depending on then value chosen, this is a different use case.
The conditional tag has "refresh_on_change" added automatically and is used by Javascript accordingly.
The feature we thought exists from the wiki docs is a utility refresh_on_change="true" attribute that you can put on any input param tag which will cause the page to refresh with the changed state when you change the param. It's supposed to replace the deprecated pages tags.
Unless there is undocumented functionality, refresh_on_change cannot be explicitly used: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
Once we started needing to make more complex form logic you realize that this is not just very useful but necessary.
Here's one example:
<inputs> <param type="data" name="dataset" refresh_on_change="true" label="Select a file from you history" /> <param type="select" multiple="true" name="dataset_values" dynamic_options="get_options_from_file(dataset.file_name)" /> </inputs>
If the user changes their selection of data from their history it should refresh the page and call the dynamic options again to load the other select menu with the choices from the new file. Currently you have to do this with repeat or pages tags which is really cumbersome for the user in the UI or doesn't allow workflowing, respectively.
Page should refresh automatically when dataset is changed and dynamic options are used. If not, it's a bug. J.
Does this feature I describe to replace the deprecated pages tags not exist or just isn't fully implemented yet?
regards, Leandro
Some questions that should shed light on your issues: *Does the Tophat tool refresh on the main server? If not, this is probably a browser issue. *Are you seeing any errors in the Javascript console? *Can you be more specific about what problems you're seeing and whether you can reproduce with known tools?
Thanks, J.
On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote:
Hi everyone,
Sorry to ping again, having the refresh_on_change functionality not working in Galaxy has us making tool forms in ways we really don't want to,
no one needs to use refresh_on_change or am I the only one that finds it's broken? We've started to look at what Galaxy is trying to do, seems like you are using jQuery to bind a custom Javascript refresh_on_change function but when you look at that function it doesn't do any form reloading, maybe just the feature is unfinished?
sincerely, Leandro
On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida <softdev@leandrohermida.com> wrote:
Hello,
Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem?
regards, Leandro
___________________________________________________________ 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:
Dear Jeremy, On Wed, Mar 21, 2012 at 1:37 PM, Jeremy Goecks <jeremy.goecks@emory.edu> wrote:
Maybe we don't understand the feature in the documentation, but this isn't the refresh_on_change functionality. In the Tophat tool XML there are no refresh_on_change="true" attributes, you are talking about a conditional tag which when changing will refresh the page in order to expose different parts of a form depending on then value chosen, this is a different use case.
The conditional tag has "refresh_on_change" added automatically and is used by Javascript accordingly.
This is understood, we use conditionals all the time, just was trying to explain that conditionals are only for certain use cases when you need to expose/hide different form elements depending on changing of a parameter. Yet there are other use cases when you need refresh_on_change functionality and not a conditional.
The feature we thought exists from the wiki docs is a utility refresh_on_change="true" attribute that you can put on any input param tag which will cause the page to refresh with the changed state when you change the param. It's supposed to replace the deprecated pages tags.
Unless there is undocumented functionality, refresh_on_change cannot be explicitly used:
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax
Once we started needing to make more complex form logic you realize that this is not just very useful but necessary.
Here's one example:
<inputs> <param type="data" name="dataset" refresh_on_change="true" label="Select a file from you history" /> <param type="select" multiple="true" name="dataset_values" dynamic_options="get_options_from_file(dataset.file_name)" /> </inputs>
If the user changes their selection of data from their history it should refresh the page and call the dynamic options again to load the other select menu with the choices from the new file. Currently you have to do this with repeat or pages tags which is really cumbersome for the user in the UI or doesn't allow workflowing, respectively.
Page should refresh automatically when dataset is changed and dynamic options are used. If not, it's a bug.
Ok, not sure what this means, the above example I wrote doesn't work so is this a bug or is there another way to write the above example so that it will work? regards, Leandro
J.
Does this feature I describe to replace the deprecated pages tags not exist or just isn't fully implemented yet?
regards, Leandro
Some questions that should shed light on your issues:
*Does the Tophat tool refresh on the main server? If not, this is probably a browser issue.
*Are you seeing any errors in the Javascript console?
*Can you be more specific about what problems you're seeing and whether you can reproduce with known tools?
Thanks,
J.
On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote:
Hi everyone,
Sorry to ping again, having the refresh_on_change functionality not
working in Galaxy has us making tool forms in ways we really don't
want to,
no one needs to use refresh_on_change or am I the only one that finds
it's broken? We've started to look at what Galaxy is trying to do,
seems like you are using jQuery to bind a custom Javascript
refresh_on_change function but when you look at that function it
doesn't do any form reloading, maybe just the feature is unfinished?
sincerely,
Leandro
On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida
<softdev@leandrohermida.com> wrote:
Hello,
Seems like the refresh_on_change functionality is broken in the latest
galaxy-dist. If you apply it to an input parameter it doesn't seem to
refresh the page when you change the selection of that parameter. Does
anyone else also have the problem?
regards,
Leandro
Leandro, For refresh_on_change to work you need a set of optional selections and a set of refresh_on_change values, so in your example, the type should probably be a select instead of data. You'll also need the select list options to be generated based on your history items (at least that's what I think you're attempt here), so your list of refresh_on_change values will be attributes of those history items. Greg Von Kuster On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote:
Here's one example:
<inputs> <param type="data" name="dataset" refresh_on_change="true" label="Select a file from you history" /> <param type="select" multiple="true" name="dataset_values" dynamic_options="get_options_from_file(dataset.file_name)" /> </inputs>
If the user changes their selection of data from their history it should refresh the page and call the dynamic options again to load the other select menu with the choices from the new file. Currently you have to do this with repeat or pages tags which is really cumbersome for the user in the UI or doesn't allow workflowing, respectively.
Page should refresh automatically when dataset is changed and dynamic options are used. If not, it's a bug.
Ok, not sure what this means, the above example I wrote doesn't work so is this a bug or is there another way to write the above example so that it will work?
regards, Leandro
___________________________________________________________ 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:
Dear Greg, On Wed, Mar 21, 2012 at 3:20 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Leandro,
For refresh_on_change to work you need a set of optional selections and a set of refresh_on_change values, so in your example, the type should probably be a select instead of data. You'll also need the select list options to be generated based on your history items (at least that's what I think you're attempt here), so your list of refresh_on_change values will be attributes of those history items.
Greg Von Kuster
Could you show an example of this functionality that you described? This is new to me I really apologize and I looked for things on the Galaxy wiki but couldn't find. How would one do the simple example I illustrated in this thread: <inputs> <param type="data" format="txt" name="dataset" label="Select a text file from you history" /> <param type="select" multiple="true" name="dataset_values" dynamic_options="get_options_from_file(dataset.file_name)" /> </inputs> Where in the tool form if the user changes the first drop-down menu to select a different file of a particular format from their history it will cause a refresh of the page so that the dynamic_options function in the second menu can be re-executed using the new file name as a parameter then generating new options in this second menu? regards, Leandro
On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote:
Here's one example:
<inputs>
<param type="data" name="dataset" refresh_on_change="true"
label="Select a file from you history" />
<param type="select" multiple="true" name="dataset_values"
dynamic_options="get_options_from_file(dataset.file_name)" />
</inputs>
If the user changes their selection of data from their history it
should refresh the page and call the dynamic options again to load the
other select menu with the choices from the new file. Currently you
have to do this with repeat or pages tags which is really cumbersome
for the user in the UI or doesn't allow workflowing, respectively.
Page should refresh automatically when dataset is changed and dynamic
options are used. If not, it's a bug.
Ok, not sure what this means, the above example I wrote doesn't work so is this a bug or is there another way to write the above example so that it will work?
regards, Leandro
___________________________________________________________ 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:
It's always best to look at examples in the code base for technical details like this rather than the wiki. You probably will need a combination of a <conditional> constructor along with a select list item in your tooll There are many tools that include these types of constructors that refresh the page when a <when> condition is met. One example is the extract_genomic_dna.xml tool config, which includes the following tag sets. <inputs> <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"/> <param name="interpret_features" type="select" label="Interpret features when possible" help="Only meaningful for GFF, GTF datasets."> <option value="yes">Yes</option> <option value="no">No</option> </param> <conditional name="seq_source"> <param name="index_source" type="select" label="Source for Genomic Data"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> </conditional> <param name="out_format" type="select" label="Output data type"> <option value="fasta">FASTA</option> <option value="interval">Interval</option> </param> </inputs> Sorry, but I don't have the time to get too much more involved in this than I have - as always, I'm stretched as thin as can be. Good luck! On Mar 22, 2012, at 5:09 AM, Leandro Hermida wrote:
Dear Greg,
On Wed, Mar 21, 2012 at 3:20 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Leandro,
For refresh_on_change to work you need a set of optional selections and a set of refresh_on_change values, so in your example, the type should probably be a select instead of data. You'll also need the select list options to be generated based on your history items (at least that's what I think you're attempt here), so your list of refresh_on_change values will be attributes of those history items.
Greg Von Kuster
Could you show an example of this functionality that you described? This is new to me I really apologize and I looked for things on the Galaxy wiki but couldn't find. How would one do the simple example I illustrated in this thread:
<inputs> <param type="data" format="txt" name="dataset" label="Select a text file from you history" /> <param type="select" multiple="true" name="dataset_values" dynamic_options="get_options_from_file(dataset.file_name)" /> </inputs>
Where in the tool form if the user changes the first drop-down menu to select a different file of a particular format from their history it will cause a refresh of the page so that the dynamic_options function in the second menu can be re-executed using the new file name as a parameter then generating new options in this second menu?
regards, Leandro
On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote:
Here's one example:
<inputs>
<param type="data" name="dataset" refresh_on_change="true"
label="Select a file from you history" />
<param type="select" multiple="true" name="dataset_values"
dynamic_options="get_options_from_file(dataset.file_name)" />
</inputs>
If the user changes their selection of data from their history it
should refresh the page and call the dynamic options again to load the
other select menu with the choices from the new file. Currently you
have to do this with repeat or pages tags which is really cumbersome
for the user in the UI or doesn't allow workflowing, respectively.
Page should refresh automatically when dataset is changed and dynamic
options are used. If not, it's a bug.
Ok, not sure what this means, the above example I wrote doesn't work so is this a bug or is there another way to write the above example so that it will work?
regards, Leandro
___________________________________________________________ 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:
___________________________________________________________ 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:
A final pointer: to see tools that use dynamic options, take a look at "Extract GFF features" and "Filter GFF dataset by feature count" Good luck, J. On Mar 22, 2012, at 12:15 PM, Greg Von Kuster wrote:
It's always best to look at examples in the code base for technical details like this rather than the wiki. You probably will need a combination of a <conditional> constructor along with a select list item in your tooll There are many tools that include these types of constructors that refresh the page when a <when> condition is met. One example is the extract_genomic_dna.xml tool config, which includes the following tag sets.
<inputs> <param format="interval,gff" name="input" type="data" label="Fetch sequences for intervals in"/> <param name="interpret_features" type="select" label="Interpret features when possible" help="Only meaningful for GFF, GTF datasets."> <option value="yes">Yes</option> <option value="no">No</option> </param> <conditional name="seq_source"> <param name="index_source" type="select" label="Source for Genomic Data"> <option value="cached">Locally cached</option> <option value="history">History</option> </param> <when value="cached"> </when> <when value="history"> <param name="ref_file" type="data" format="fasta" label="Using reference file" /> </when> </conditional> <param name="out_format" type="select" label="Output data type"> <option value="fasta">FASTA</option> <option value="interval">Interval</option> </param> </inputs>
Sorry, but I don't have the time to get too much more involved in this than I have - as always, I'm stretched as thin as can be. Good luck!
On Mar 22, 2012, at 5:09 AM, Leandro Hermida wrote:
Dear Greg,
On Wed, Mar 21, 2012 at 3:20 PM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Leandro,
For refresh_on_change to work you need a set of optional selections and a set of refresh_on_change values, so in your example, the type should probably be a select instead of data. You'll also need the select list options to be generated based on your history items (at least that's what I think you're attempt here), so your list of refresh_on_change values will be attributes of those history items.
Greg Von Kuster
Could you show an example of this functionality that you described? This is new to me I really apologize and I looked for things on the Galaxy wiki but couldn't find. How would one do the simple example I illustrated in this thread:
<inputs> <param type="data" format="txt" name="dataset" label="Select a text file from you history" /> <param type="select" multiple="true" name="dataset_values" dynamic_options="get_options_from_file(dataset.file_name)" /> </inputs>
Where in the tool form if the user changes the first drop-down menu to select a different file of a particular format from their history it will cause a refresh of the page so that the dynamic_options function in the second menu can be re-executed using the new file name as a parameter then generating new options in this second menu?
regards, Leandro
On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote:
Here's one example:
<inputs>
<param type="data" name="dataset" refresh_on_change="true"
label="Select a file from you history" />
<param type="select" multiple="true" name="dataset_values"
dynamic_options="get_options_from_file(dataset.file_name)" />
</inputs>
If the user changes their selection of data from their history it
should refresh the page and call the dynamic options again to load the
other select menu with the choices from the new file. Currently you
have to do this with repeat or pages tags which is really cumbersome
for the user in the UI or doesn't allow workflowing, respectively.
Page should refresh automatically when dataset is changed and dynamic
options are used. If not, it's a bug.
Ok, not sure what this means, the above example I wrote doesn't work so is this a bug or is there another way to write the above example so that it will work?
regards, Leandro
___________________________________________________________ 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:
___________________________________________________________ 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:
___________________________________________________________ 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:
participants (3)
-
Greg Von Kuster -
Jeremy Goecks -
Leandro Hermida