Fwd: Your message to galaxy-dev awaits moderator approval
---------- Forwarded message ---------- From: <galaxy-dev-bounces@lists.bx.psu.edu> Date: Mon, May 23, 2011 at 11:42 AM Subject: Your message to galaxy-dev awaits moderator approval To: meshashi29@gmail.com Your mail to 'galaxy-dev' with the subject requirement of complete command in code file Is being held until the list moderator can review it for approval. The reason it is being held: Post by non-member to a members-only list Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL: http://lists.bx.psu.edu/confirm/galaxy-dev/32ca9fa0742b2f4b3a3e5ad2f9c57f067...
I have also been getting such messages and even saying there are too many re-bounces so your account is being disabled and I can not reactivate using the link sent in email On Sun, May 22, 2011 at 11:28 PM, shashi shekhar <meshashi29@gmail.com>wrote:
---------- Forwarded message ---------- From: <galaxy-dev-bounces@lists.bx.psu.edu> Date: Mon, May 23, 2011 at 11:42 AM Subject: Your message to galaxy-dev awaits moderator approval To: meshashi29@gmail.com
Your mail to 'galaxy-dev' with the subject
requirement of complete command in code file
Is being held until the list moderator can review it for approval.
The reason it is being held:
Post by non-member to a members-only list
Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL:
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Hello, I know this is still not fully implemented and that there has already been a lot of messages on the topic, but I just would like to know if there's a way to make the "checked" attribute in the param tags have the required effect. Regards, L-A PS: looking forward to seeing the conference in Lunteren :)
2011/5/23 Louise-Amélie Schmitt <louise-amelie.schmitt@embl.de>:
Hello,
I know this is still not fully implemented and that there has already been a lot of messages on the topic, but I just would like to know if there's a way to make the "checked" attribute in the param tags have the required effect.
It might help if you were more precise - what isn't working for you? Ideally there would be an issue already reported on this on bitbucket. https://bitbucket.org/galaxy/galaxy-central/issues?sort=-id As I recall, the checked attribute is working fine for boolean parameters: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Peter
Not everything works correctly with checkbox booleans, the bug a couple people and I reported long ago https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-bool... is still there. 2011/5/23 Peter Cock <p.j.a.cock@googlemail.com>
2011/5/23 Louise-Amélie Schmitt <louise-amelie.schmitt@embl.de>:
Hello,
I know this is still not fully implemented and that there has already been a lot of messages on the topic, but I just would like to know if there's a way to make the "checked" attribute in the param tags have the required effect.
It might help if you were more precise - what isn't working for you?
Ideally there would be an issue already reported on this on bitbucket. https://bitbucket.org/galaxy/galaxy-central/issues?sort=-id
As I recall, the checked attribute is working fine for boolean parameters: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
Peter
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@ Peter: I'm not sure I can get more precise... the checked attribute has no effect whatsoever, the boxes are always unchecked when I open the tool. I tried the "yes" and the "true" values to no avail. @ Leandro: Yes I already saw that and tried to correct the code the way someone suggested in the mailing list archives: http://lists.bx.psu.edu/pipermail/galaxy-dev/attachments/20100924/03979abb/a... But since I couldn't get it working I found another way to do what I want. But that's actually not the issue here. I just want my checkboxes to be checked by default, and it appears not to work. To give an example, here is one of the lines of my tool XML file: <param name="SQA" type="boolean" label="Run SolexaQA" checked="true" /> This checkbox remains unchecked at tool opening. As far as I know, some people managed to get it working and I'd like to know how. Any suggestion? Thanks, L-A Le 23/05/2011 16:29, Leandro Hermida a écrit :
Not everything works correctly with checkbox booleans, the bug a couple people and I reported long ago
https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-bool...
is still there.
2011/5/23 Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>>
2011/5/23 Louise-Amélie Schmitt <louise-amelie.schmitt@embl.de <mailto:louise-amelie.schmitt@embl.de>>: > Hello, > > I know this is still not fully implemented and that there has already been a > lot of messages on the topic, but I just would like to know if there's a way > to make the "checked" attribute in the param tags have the required effect.
It might help if you were more precise - what isn't working for you?
Ideally there would be an issue already reported on this on bitbucket. https://bitbucket.org/galaxy/galaxy-central/issues?sort=-id
As I recall, the checked attribute is working fine for boolean parameters: https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax
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:
2011/5/23 Louise-Amélie Schmitt <louise-amelie.schmitt@embl.de>:
@ Peter: I'm not sure I can get more precise... the checked attribute has no effect whatsoever, the boxes are always unchecked when I open the tool. I tried the "yes" and the "true" values to no avail.
@ Leandro: Yes I already saw that ...
But that's actually not the issue here. I just want my checkboxes to be checked by default, and it appears not to work.
To give an example, here is one of the lines of my tool XML file: <param name="SQA" type="boolean" label="Run SolexaQA" checked="true" /> This checkbox remains unchecked at tool opening.
As far as I know, some people managed to get it working and I'd like to know how.
Any suggestion?
I think you've found a bug :( I found two working examples, "Filter out low complexity regions (with DUST)" parameter in tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml and the scaffolding parameter in sr_assembly/velvetg.xml - however they are both within a conditional parameter section (only shown in advanced mode). Have a look at sr_mapping/bwa_color_wrapper.xml which has a "Suppress the header in the output SAM file" boolean which should be checked by default: <param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" /> It's not working on http://usegalaxy.org - the box isn't checked. If you can verify that, please file an issue on bitbucket: https://bitbucket.org/galaxy/galaxy-central/issues/new Peter
Yeah, and I fixed it... somehow. In the lib/galaxy/web/form_builder.py I added the import on string_as_bool from galaxy.util, then I modified the code as follows: 126 @staticmethod 127 def is_checked( value ): 128 if value == True: 129 return True 130 # This may look strange upon initial inspection, but see the comments in the get_html() method 131 # above for clarification. Basically, if value is not True, then it will always be a list with 132 # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not 133 # checked, then value will be only the hidden field. 134 if isinstance(value, basestring): 135 return string_as_bool( value ) 136 return isinstance( value, list ) and len( value ) == 2 (see l.134 and 135) The value variable actually contained something else than True or a list, namely the string "true". Now it seems to work fine. Cheers, L-A Le 23/05/2011 18:26, Peter Cock a écrit :
2011/5/23 Louise-Amélie Schmitt<louise-amelie.schmitt@embl.de>:
@ Peter: I'm not sure I can get more precise... the checked attribute has no effect whatsoever, the boxes are always unchecked when I open the tool. I tried the "yes" and the "true" values to no avail.
@ Leandro: Yes I already saw that ...
But that's actually not the issue here. I just want my checkboxes to be checked by default, and it appears not to work.
To give an example, here is one of the lines of my tool XML file: <param name="SQA" type="boolean" label="Run SolexaQA" checked="true" /> This checkbox remains unchecked at tool opening.
As far as I know, some people managed to get it working and I'd like to know how.
Any suggestion? I think you've found a bug :(
I found two working examples, "Filter out low complexity regions (with DUST)" parameter in tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml and the scaffolding parameter in sr_assembly/velvetg.xml - however they are both within a conditional parameter section (only shown in advanced mode).
Have a look at sr_mapping/bwa_color_wrapper.xml which has a "Suppress the header in the output SAM file" boolean which should be checked by default:
<param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
It's not working on http://usegalaxy.org - the box isn't checked.
If you can verify that, please file an issue on bitbucket: https://bitbucket.org/galaxy/galaxy-central/issues/new
Peter
Thanks! This has been fixed in changeset 5594:2f84c42a548a. Also, if I could ask for a minor thing to assist us with list maintenance: when starting a new thread on the list, please create a brand new email to galaxy-dev rather than replying to an existing message. Replying includes headers that reference the message you replied to, which means it threads with the original thread in mail readers and the list archive. Thanks, --nate Louise-Amélie Schmitt wrote:
Yeah, and I fixed it... somehow.
In the lib/galaxy/web/form_builder.py I added the import on string_as_bool from galaxy.util, then I modified the code as follows:
126 @staticmethod 127 def is_checked( value ): 128 if value == True: 129 return True 130 # This may look strange upon initial inspection, but see the comments in the get_html() method 131 # above for clarification. Basically, if value is not True, then it will always be a list with 132 # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not 133 # checked, then value will be only the hidden field. 134 if isinstance(value, basestring): 135 return string_as_bool( value ) 136 return isinstance( value, list ) and len( value ) == 2
(see l.134 and 135) The value variable actually contained something else than True or a list, namely the string "true". Now it seems to work fine.
Cheers, L-A
Le 23/05/2011 18:26, Peter Cock a écrit :
2011/5/23 Louise-Amélie Schmitt<louise-amelie.schmitt@embl.de>:
@ Peter: I'm not sure I can get more precise... the checked attribute has no effect whatsoever, the boxes are always unchecked when I open the tool. I tried the "yes" and the "true" values to no avail.
@ Leandro: Yes I already saw that ...
But that's actually not the issue here. I just want my checkboxes to be checked by default, and it appears not to work.
To give an example, here is one of the lines of my tool XML file: <param name="SQA" type="boolean" label="Run SolexaQA" checked="true" /> This checkbox remains unchecked at tool opening.
As far as I know, some people managed to get it working and I'd like to know how.
Any suggestion? I think you've found a bug :(
I found two working examples, "Filter out low complexity regions (with DUST)" parameter in tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml and the scaffolding parameter in sr_assembly/velvetg.xml - however they are both within a conditional parameter section (only shown in advanced mode).
Have a look at sr_mapping/bwa_color_wrapper.xml which has a "Suppress the header in the output SAM file" boolean which should be checked by default:
<param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
It's not working on http://usegalaxy.org - the box isn't checked.
If you can verify that, please file an issue on bitbucket: https://bitbucket.org/galaxy/galaxy-central/issues/new
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:
Ok, no problem, I really didn't notice. Really sorry about that. I'll be careful from now on. Thanks for the add in the changeset but I suspect the problem should be fixed somewhere else, I mean upstream since the value variable doesn't receive the appropriate stuff. I didn't quite get where it comes from though. Looking forward to seeing you in Lunteren :) Regards, L-A Le 24/05/2011 11:38, Nate Coraor a écrit :
Thanks! This has been fixed in changeset 5594:2f84c42a548a.
Also, if I could ask for a minor thing to assist us with list maintenance: when starting a new thread on the list, please create a brand new email to galaxy-dev rather than replying to an existing message. Replying includes headers that reference the message you replied to, which means it threads with the original thread in mail readers and the list archive.
Thanks, --nate
Louise-Amélie Schmitt wrote:
Yeah, and I fixed it... somehow.
In the lib/galaxy/web/form_builder.py I added the import on string_as_bool from galaxy.util, then I modified the code as follows:
126 @staticmethod 127 def is_checked( value ): 128 if value == True: 129 return True 130 # This may look strange upon initial inspection, but see the comments in the get_html() method 131 # above for clarification. Basically, if value is not True, then it will always be a list with 132 # 2 input fields ( a checkbox and a hidden field ) if the checkbox is checked. If it is not 133 # checked, then value will be only the hidden field. 134 if isinstance(value, basestring): 135 return string_as_bool( value ) 136 return isinstance( value, list ) and len( value ) == 2
(see l.134 and 135) The value variable actually contained something else than True or a list, namely the string "true". Now it seems to work fine.
Cheers, L-A
Le 23/05/2011 18:26, Peter Cock a écrit :
2011/5/23 Louise-Amélie Schmitt<louise-amelie.schmitt@embl.de>:
@ Peter: I'm not sure I can get more precise... the checked attribute has no effect whatsoever, the boxes are always unchecked when I open the tool. I tried the "yes" and the "true" values to no avail.
@ Leandro: Yes I already saw that ...
But that's actually not the issue here. I just want my checkboxes to be checked by default, and it appears not to work.
To give an example, here is one of the lines of my tool XML file: <param name="SQA" type="boolean" label="Run SolexaQA" checked="true" /> This checkbox remains unchecked at tool opening.
As far as I know, some people managed to get it working and I'd like to know how.
Any suggestion? I think you've found a bug :(
I found two working examples, "Filter out low complexity regions (with DUST)" parameter in tools/ncbi_blast_plus/ncbi_blastn_wrapper.xml and the scaffolding parameter in sr_assembly/velvetg.xml - however they are both within a conditional parameter section (only shown in advanced mode).
Have a look at sr_mapping/bwa_color_wrapper.xml which has a "Suppress the header in the output SAM file" boolean which should be checked by default:
<param name="suppressHeader" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Suppress the header in the output SAM file" help="BWA produces SAM with several lines of header information" />
It's not working on http://usegalaxy.org - the box isn't checked.
If you can verify that, please file an issue on bitbucket: https://bitbucket.org/galaxy/galaxy-central/issues/new
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:
Hi, In the case of the original email from Shashi, it would appear that the email address used was not the one subscribed to the mailing list. We'll have a look at your subscription to see if there's an issue. Thanks, --nate shamsher jagat wrote:
I have also been getting such messages and even saying there are too many re-bounces so your account is being disabled and I can not reactivate using the link sent in email
On Sun, May 22, 2011 at 11:28 PM, shashi shekhar <meshashi29@gmail.com>wrote:
---------- Forwarded message ---------- From: <galaxy-dev-bounces@lists.bx.psu.edu> Date: Mon, May 23, 2011 at 11:42 AM Subject: Your message to galaxy-dev awaits moderator approval To: meshashi29@gmail.com
Your mail to 'galaxy-dev' with the subject
requirement of complete command in code file
Is being held until the list moderator can review it for approval.
The reason it is being held:
Post by non-member to a members-only list
Either the message will get posted to the list, or you will receive notification of the moderator's decision. If you would like to cancel this posting, please visit the following URL:
http://lists.bx.psu.edu/confirm/galaxy-dev/32ca9fa0742b2f4b3a3e5ad2f9c57f067...
___________________________________________________________ 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 (6)
-
Leandro Hermida -
Louise-Amélie Schmitt -
Nate Coraor -
Peter Cock -
shamsher jagat -
shashi shekhar