Re: [galaxy-dev] checkboxes bug fix
Hi Kanwei, and thanks for your reply. I might have missed something really big but I'm kinda confused. I just double checked galaxy-dist and galaxy-central on bitbucket and I would like to know if I understood the code properly. Please correct me if I'm wrong. Let's look at the is_checked() method of the CheckboxField class in the lib/galaxy/web/form_builder.py file: If I'm not mistaken, it relies on the fact that if the checkbox is checked, the request will get two values (the checkbox and the hidden field) and if it is not, it will only get one value (the hidden field) since they bear the same name. The first part is the conditional that checks if the value is True: That means that there is only one value, so the checkbox must be unchecked. Therefore it tests the hidden field's value. It will return True if the hidden field's value is true. The second part is only executed if the above condition is false: this means either the checkbox is actually checked, or it is unchecked and the hidden field is false. It returns true if there are two values, i.e. if the checkbox is checked. If the hidden field is false, it will obviously return False. So, let's see both cases: - 1st case: the hidden field is true: If the checkbox is unchecked, the method will return True in the first part. If it is checked, it will also return True in the second part. - 2d case: the hidden field is false: If the checkbox is checked, like in the 1st case, the second part will return True. But if it is unchecked, the first part won't return anything since the received value is not True. So it will return the result of the second part which is false since False is not an instance of list. Now my questions are: Did I miss anything? If not, how can the first case work for you? Wouldn't there be some cases where a checkbox actually gives a value even if it is unchecked, and a field is ignored of there is already one with the same name? Thanks, L-A Le 24/08/2011 19:36, Kanwei Li a écrit : Hi L-A, I tried this on today's tip but could not reproduce the bug. I added your param param name=SQA type=boolean label=Run SolexaQA checked=true / to a tool and the correct value was produced on the command line and in the configfiles block as well. Re-running also gave the correct result. Are you still seeing this problem? Thanks, K 2011/8/15 Louise-Amélie Schmitt louise-amelie.schm...@embl.de mailto:louise-amelie.schm...@embl.de Hello, Sorry for being late, again, but please find the tool attached. Here is my last pull: 5743:720455407d1c Stuff changed in the file but in the end I had to make the same modification again (change true to false) since it didn't work anymore. Best, L-A Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit : Hi, and sorry for the late reply Here is the last pull: 5355:50e249442c5a I'll try to be as concise as I can but I can send you the whole file if you need it. It's not completely done yet though. This is a tool that produces a HTML file containing the results of various quality assessment programs. To trigger or block the execution of a specific program, I use checkboxes in the form, like this: param name=SQA type=boolean label=Run SolexaQA checked=true / Then, I use the configfile name=script tags to define a shell script that will be modified with cheetah tests on the checkboxes. Then the final script is sent to another shell script that will check its existence and launch it: command interpreter='sh'all_QA.sh $script /command As you can see, the checkboxes are checked by default. But before the change I mentioned is my last email, un-checking them didn't have any effect whatsoever. The following test, for instance, was always true: #if $SQA.value == True Moreover, even if I un-checked the checkboxes and ran the tool, then clicked the re-run button in the result in my history, all of them were checked in the form that appears, as if I never un-checked them. Now, the state of the checkboxes is respected and I can properly choose what to run in my tool. Hope that helps. L-A Le 08/06/2011 20:54, Jennifer Jackson a écrit : Hi L-A, Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected
Re: [galaxy-dev] checkboxes bug fix
Hi L-A, I tried this on today's tip but could not reproduce the bug. I added your param param name=SQA type=boolean label=Run SolexaQA checked=true / to a tool and the correct value was produced on the command line and in the configfiles block as well. Re-running also gave the correct result. Are you still seeing this problem? Thanks, K 2011/8/15 Louise-Amélie Schmitt louise-amelie.schm...@embl.de Hello, Sorry for being late, again, but please find the tool attached. Here is my last pull: 5743:720455407d1c Stuff changed in the file but in the end I had to make the same modification again (change true to false) since it didn't work anymore. Best, L-A Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit : Hi, and sorry for the late reply Here is the last pull: 5355:50e249442c5a I'll try to be as concise as I can but I can send you the whole file if you need it. It's not completely done yet though. This is a tool that produces a HTML file containing the results of various quality assessment programs. To trigger or block the execution of a specific program, I use checkboxes in the form, like this: param name=SQA type=boolean label=Run SolexaQA checked=true / Then, I use the configfile name=script tags to define a shell script that will be modified with cheetah tests on the checkboxes. Then the final script is sent to another shell script that will check its existence and launch it: command interpreter='sh'all_QA.sh $script /command As you can see, the checkboxes are checked by default. But before the change I mentioned is my last email, un-checking them didn't have any effect whatsoever. The following test, for instance, was always true: #if $SQA.value == True Moreover, even if I un-checked the checkboxes and ran the tool, then clicked the re-run button in the result in my history, all of them were checked in the form that appears, as if I never un-checked them. Now, the state of the checkboxes is respected and I can properly choose what to run in my tool. Hope that helps. L-A Le 08/06/2011 20:54, Jennifer Jackson a écrit : Hi L-A, Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=true%s' \ for: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=false%s' \ And it works fine now :) Cheers, L-A __**_ 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/ __**_ 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/ ___ 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/ ___ 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/
Re: [galaxy-dev] checkboxes bug fix
Hello, Sorry for being late, again, but please find the tool attached. Here is my last pull: 5743:720455407d1c Stuff changed in the file but in the end I had to make the same modification again (change true to false) since it didn't work anymore. Best, L-A Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit : Hi, and sorry for the late reply Here is the last pull: 5355:50e249442c5a I'll try to be as concise as I can but I can send you the whole file if you need it. It's not completely done yet though. This is a tool that produces a HTML file containing the results of various quality assessment programs. To trigger or block the execution of a specific program, I use checkboxes in the form, like this: param name=SQA type=boolean label=Run SolexaQA checked=true / Then, I use the configfile name=script tags to define a shell script that will be modified with cheetah tests on the checkboxes. Then the final script is sent to another shell script that will check its existence and launch it: command interpreter='sh'all_QA.sh $script /command As you can see, the checkboxes are checked by default. But before the change I mentioned is my last email, un-checking them didn't have any effect whatsoever. The following test, for instance, was always true: #if $SQA.value == True Moreover, even if I un-checked the checkboxes and ran the tool, then clicked the re-run button in the result in my history, all of them were checked in the form that appears, as if I never un-checked them. Now, the state of the checkboxes is respected and I can properly choose what to run in my tool. Hope that helps. L-A Le 08/06/2011 20:54, Jennifer Jackson a écrit : Hi L-A, Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=true%s' \ for: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=false%s' \ And it works fine now :) Cheers, L-A ___ 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/ ___ 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/ tool id=all_QA name=QA Bundle description=performs multiple QA command interpreter='sh'all_QA.sh $script /command inputs param name=input type=data label=Input file format=fastq,fastqillumina,sam,export,bam checked=true / param name=R type=boolean label=Run R QA (runs only on export files) checked=true / param name=HTSeq type=boolean label=Run HTSeq QA checked=true / param name=C type=boolean label=Run baseQual (work only with fastq files) checked=true / param name=SQA type=boolean label=Run SolexaQA checked=true / param type=select name=SQA_cutoff label=#60;span style=#34;font-weight:normal;#34;#62;Cutoff (phred value at which base-calling error is considered too high)#60;/span#62; help= option value=1010 (90%)/option option value=13 selected=true13 (95%)/option option value=2020 (99%)/option option value=3030 (99.9%)/option option value=4040 (99.99%)/option /param param type=select name=SQA_variance label=#60;span style=#34;font-weight:normal;#34;#62;Calculate variance statistics#60;/span#62; display=radio help= option value= selected=trueNo thanks/option option value=-vYes please/option /param param type=select name=SQA_minmax label=#60;span style=#34;font-weight:normal;#34;#62;Calculate minimum and maximum error probabilities for each read position of each tile#60;/span#62; display=radio help= option value= selected=trueNo thanks/option option value=-mYes please/option /param param name=SQA_sample size=6 type=integer value=1 label=#60;span style=#34;font-weight:normal;#34;#62;Number of sequences to be sampled per tile for satistic estimates#60;/span#62; help= / param name=CovE type=boolean label=Run Coverage Estimation checked=true / param type=select name=window label=#60;span style=#34;font-weight:normal;#34;#62;Windows size for
Re: [galaxy-dev] checkboxes bug fix
Hi L-A, Could you describe a use case (which tool/from, what options/input)? If you know the last pull # for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=true%s' \ for: 105 return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=false%s' \ And it works fine now :) Cheers, L-A ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org ___ 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/
[galaxy-dev] checkboxes bug fix
Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were selected as if I never deselected them. Therefore, in lib/galaxy/web/form_builder.py I changed: 105return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=true%s' \ for: 105return 'input type=checkbox id=%s name=%s value=true%s%sinput type=hidden name=%s%s value=false%s' \ And it works fine now :) Cheers, L-A ___ 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/
