GBrowse_syn bug report

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GBrowse_syn bug report

Hyunmin Kim
Hi, All

I think my finding is bug on GBrowse_syn.

For example, when I set the sample chromosome (scaffold or config..etc) name is gallus-4.
[Genome to search: ] can't be auto selection.

Maybe it caused by naming ( involve “-“ in chromosome name).

Test URL:

Tutorial (For find the bug)

2. Click the example: [hg19 chr4:159567935..159567940]

3. and Click the another example: [gallus-4 4:93742817..93742820]

and you’ll get the error message:

Species 'gallus-4' is not configured for this database

so, you must select the [Genome to search: ] to gallus-4
and you’ll can show the correct result.


If you don’t understand my reporting, please reply to me.

Thanks,
Hyunmin

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Re: GBrowse_syn bug report

Sheldon McKay
Hi Hyunmin,

Would you mind sharing your main configuration file (the one with something similar to the text below) so I can try to reproduce your error?

Sheldon


#                 name          conf. file            Description
source_map =     rice         rice_synteny          "Domesic Rice (O. sativa)"
                          wild_rice     wild_rice_synteny     "Wild Rice"


On Tue, Apr 29, 2014 at 2:34 AM, Hyunmin Kim <[hidden email]> wrote:
Hi, All

I think my finding is bug on GBrowse_syn.

For example, when I set the sample chromosome (scaffold or config..etc) name is gallus-4.
[Genome to search: ] can't be auto selection.

Maybe it caused by naming ( involve “-“ in chromosome name).

Test URL:

Tutorial (For find the bug)

2. Click the example: [hg19 chr4:159567935..159567940]

3. and Click the another example: [gallus-4 4:93742817..93742820]

and you’ll get the error message:

Species 'gallus-4' is not configured for this database

<form method="post" action="http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/test_syn/?search_src=gallus-4;name=4:93742817..93742820" enctype="multipart/form-data" name="145ac31e2ea811df_searchform" style="font-family:sans-serif;font-size:small" target="_blank" onsubmit="return window.confirm(&quot;You are submitting information to an external page.\nAre you sure?&quot;);">
so, you must select the [Genome to search: ] to gallus-4
and you’ll can show the correct result.


If you don’t understand my reporting, please reply to me.

Thanks,
Hyunmin

------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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unparalleled scalability from the best Selenium testing platform available.
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Re: GBrowse_syn bug report

Hyunmin Kim
Here is my synteny config file.

Refer to attached file.



Hyunmin

2014. 4. 29., 오후 7:51, Sheldon McKay <[hidden email]> 작성:

Hi Hyunmin,

Would you mind sharing your main configuration file (the one with something similar to the text below) so I can try to reproduce your error?

Sheldon


#                 name          conf. file            Description
source_map =     rice         rice_synteny          "Domesic Rice (O. sativa)"
                          wild_rice     wild_rice_synteny     "Wild Rice"


On Tue, Apr 29, 2014 at 2:34 AM, Hyunmin Kim <[hidden email]> wrote:
Hi, All

I think my finding is bug on GBrowse_syn.

For example, when I set the sample chromosome (scaffold or config..etc) name is gallus-4.
[Genome to search: ] can't be auto selection.

Maybe it caused by naming ( involve “-“ in chromosome name).

Test URL:

Tutorial (For find the bug)

2. Click the example: [hg19 chr4:159567935..159567940]

3. and Click the another example: [gallus-4 4:93742817..93742820]

and you’ll get the error message:

Species 'gallus-4' is not configured for this database

<form method="post" action="http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/test_syn/?search_src=gallus-4;name=4:93742817..93742820" enctype="multipart/form-data" name="145ac31e2ea811df_searchform" style="font-family:sans-serif;font-size:small" target="_blank" onsubmit="return window.confirm(&quot;You are submitting information to an external page.\nAre you sure?&quot;);">
so, you must select the [Genome to search: ] to gallus-4
and you’ll can show the correct result.


If you don’t understand my reporting, please reply to me.

Thanks,
Hyunmin

------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse




------------------------------------------------------------------------------
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Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
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test_syn.synconf (1K) Download Attachment
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Re: GBrowse_syn bug report

Sheldon McKay
Hi Hyunmin,

What you are observing is an intended behavior.  From your configuration, which I have pasted below, you have gallus-4 set as your human-readable description of the data source in the third column.  However, in the first column, the name of the data source (species) is still gallus. In the "example" syntax of the configuration page, the first value id the name of the data source, rather than it's free form text description.  (eg: gallus4 :93742817..93742820).  On the web page, what you see in the pull-down menu for 'Genome to search:' is the description, but the value passed to gbrowse_syn is the name.

On your web site, compare:
with


#                 name          conf. file            Description
source_map =      hg19          hg19_synteny          "hg19"
                  gallus        gallus_synteny        "gallus-4"



On Tue, Apr 29, 2014 at 9:20 PM, Hyunmin Kim <[hidden email]> wrote:
Here is my synteny config file.

Refer to attached file.



Hyunmin

2014. 4. 29., 오후 7:51, Sheldon McKay <[hidden email]> 작성:

Hi Hyunmin,

Would you mind sharing your main configuration file (the one with something similar to the text below) so I can try to reproduce your error?

Sheldon


#                 name          conf. file            Description
source_map =     rice         rice_synteny          "Domesic Rice (O. sativa)"
                          wild_rice     wild_rice_synteny     "Wild Rice"


On Tue, Apr 29, 2014 at 2:34 AM, Hyunmin Kim <[hidden email]> wrote:
Hi, All

I think my finding is bug on GBrowse_syn.

For example, when I set the sample chromosome (scaffold or config..etc) name is gallus-4.
[Genome to search: ] can't be auto selection.

Maybe it caused by naming ( involve “-“ in chromosome name).

Test URL:

Tutorial (For find the bug)

2. Click the example: [hg19 chr4:159567935..159567940]

3. and Click the another example: [gallus-4 4:93742817..93742820]

and you’ll get the error message:

Species 'gallus-4' is not configured for this database

<form method="post" action="http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/test_syn/?search_src=gallus-4;name=4:93742817..93742820" enctype="multipart/form-data" name="145b03873f828a1a_145ac31e2ea811df_searchform" style="font-family:sans-serif;font-size:small" target="_blank" onsubmit="return window.confirm(&quot;You are submitting information to an external page.\nAre you sure?&quot;);">
so, you must select the [Genome to search: ] to gallus-4
and you’ll can show the correct result.


If you don’t understand my reporting, please reply to me.

Thanks,
Hyunmin

------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Gmod-gbrowse mailing list
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https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse






------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
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Re: GBrowse_syn bug report

Hyunmin Kim
Dear, Sheldon

Yes, I solve this problem.

I’m sorry it’s my mistake understanding.

Thanks for your observing.

Hyunmin

2014. 4. 30., 오전 10:40, Sheldon McKay <[hidden email]> 작성:

Hi Hyunmin,

What you are observing is an intended behavior.  From your configuration, which I have pasted below, you have gallus-4 set as your human-readable description of the data source in the third column.  However, in the first column, the name of the data source (species) is still gallus. In the "example" syntax of the configuration page, the first value id the name of the data source, rather than it's free form text description.  (eg: gallus4 :93742817..93742820).  On the web page, what you see in the pull-down menu for 'Genome to search:' is the description, but the value passed to gbrowse_syn is the name.

On your web site, compare:
with


#                 name          conf. file            Description
source_map =      hg19          hg19_synteny          "hg19"
                  gallus        gallus_synteny        "gallus-4"



On Tue, Apr 29, 2014 at 9:20 PM, Hyunmin Kim <[hidden email]> wrote:
Here is my synteny config file.

Refer to attached file.



Hyunmin

2014. 4. 29., 오후 7:51, Sheldon McKay <[hidden email]> 작성:

Hi Hyunmin,

Would you mind sharing your main configuration file (the one with something similar to the text below) so I can try to reproduce your error?

Sheldon


#                 name          conf. file            Description
source_map =     rice         rice_synteny          "Domesic Rice (O. sativa)"
                          wild_rice     wild_rice_synteny     "Wild Rice"


On Tue, Apr 29, 2014 at 2:34 AM, Hyunmin Kim <[hidden email]> wrote:
Hi, All

I think my finding is bug on GBrowse_syn.

For example, when I set the sample chromosome (scaffold or config..etc) name is gallus-4.
[Genome to search: ] can't be auto selection.

Maybe it caused by naming ( involve “-“ in chromosome name).

Test URL:

Tutorial (For find the bug)

2. Click the example: [hg19 chr4:159567935..159567940]

3. and Click the another example: [gallus-4 4:93742817..93742820]

and you’ll get the error message:

Species 'gallus-4' is not configured for this database

<form method="post" action="http://182.162.88.52/cgi-bin/gb2/gbrowse_syn/test_syn/?search_src=gallus-4;name=4:93742817..93742820" enctype="multipart/form-data" name="145b03873f828a1a_145ac31e2ea811df_searchform" style="font-family:sans-serif;font-size:small" target="_blank" onsubmit="return window.confirm(&quot;You are submitting information to an external page.\nAre you sure?&quot;);">
so, you must select the [Genome to search: ] to gallus-4
and you’ll can show the correct result.


If you don’t understand my reporting, please reply to me.

Thanks,
Hyunmin

------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
Gmod-gbrowse mailing list
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------------------------------------------------------------------------------
"Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE
Instantly run your Selenium tests across 300+ browser/OS combos.  Get
unparalleled scalability from the best Selenium testing platform available.
Simple to use. Nothing to install. Get started now for free."
http://p.sf.net/sfu/SauceLabs
_______________________________________________
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