Problem With Custom Track Entries in the Uploads Table of the Users.SQLite Database

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Problem With Custom Track Entries in the Uploads Table of the Users.SQLite Database

Cruncher
Hi Guys,

I'm uploading large files to GBrowse manually as custom tracks. I've written scripts to create the sqlite database for the upload, the proper folder structure under "userdata", and the entry in the users.sqlite database.

The directory structure that is created looks like this:
userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite  
                STATUS     
                feature_name.conf  
                SOURCES/
                    feature_name


The upload seems to work fine and the new track appears under "Custom Tracks" as shown in the following screenshot:
Inline image 1

here "might-have-fixed-the-featurefile" is the new upload.

But the upload is not shown under "Select Tracks":
Inline image 2

I've done a bit of troubleshooting to try to figure out why this is happening. I've narrowed the problem down to the entry in the "uploads" table of the "users.sqlite" database.
These are the current entries in the database:

"2","private","trying-again",                            "","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again",                            "0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile","0"

I included the "trying-again" entry as a working example for reference.
note: the trackid is 32 characters long for both


As far as I can tell there is no difference between the two entries, but if I point the working "trying-again" entry at the non-working "might-have-fixed-the-featurefile" path like so:

"2","private","might-have-fixed-the-featurefile","","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again showing might-have-fixed-the-featurefile","0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile",                               "0"

My initially non-working track is displayed properly:
Inline image 3

Which tells me that the folder structure, sqlite sqlite database, and configuration for my new custom track are being created properly but there is some problem with the entry in the "uploads" table of the users.sqlite database preventing the track from being displayed properly.


Does anyone have any idea what may be wrong with the "uploads" entries that my script is creating?


Thanks,
Brad


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Re: Problem With Custom Track Entries in the Uploads Table of the Users.SQLite Database

Cruncher
After further testing I was able to narrow it down to a problem with the trackids that my script is creating. Is there some specific formatting that these IDs need to follow? Currently I'm just creating random 32 character alphanumeric strings.

Thanks,
Brad


On Thu, Apr 10, 2014 at 11:44 AM, Brad Covey <[hidden email]> wrote:
Hi Guys,

I'm uploading large files to GBrowse manually as custom tracks. I've written scripts to create the sqlite database for the upload, the proper folder structure under "userdata", and the entry in the users.sqlite database.

The directory structure that is created looks like this:
userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite  
                STATUS     
                feature_name.conf  
                SOURCES/
                    feature_name


The upload seems to work fine and the new track appears under "Custom Tracks" as shown in the following screenshot:
Inline image 1

here "might-have-fixed-the-featurefile" is the new upload.

But the upload is not shown under "Select Tracks":
Inline image 2

I've done a bit of troubleshooting to try to figure out why this is happening. I've narrowed the problem down to the entry in the "uploads" table of the "users.sqlite" database.
These are the current entries in the database:

"2","private","trying-again",                            "","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again",                            "0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile","0"

I included the "trying-again" entry as a working example for reference.
note: the trackid is 32 characters long for both


As far as I can tell there is no difference between the two entries, but if I point the working "trying-again" entry at the non-working "might-have-fixed-the-featurefile" path like so:

"2","private","might-have-fixed-the-featurefile","","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again showing might-have-fixed-the-featurefile","0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile",                               "0"

My initially non-working track is displayed properly:
Inline image 3

Which tells me that the folder structure, sqlite sqlite database, and configuration for my new custom track are being created properly but there is some problem with the entry in the "uploads" table of the users.sqlite database preventing the track from being displayed properly.


Does anyone have any idea what may be wrong with the "uploads" entries that my script is creating?


Thanks,
Brad



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volvox tutorial conf files

Matthew Johnson
Hey Guys,

I’ve started the tutorial and setup the volvox database and configured the gbrowse.conf to point to the volvox.conf.  The bottom of my volvox.conf reads:

[ExampleFeatures]
feature      = remark
glyph        = generic
stranded     = 1
bgcolor      = blue
height       = 10
key          = Example Features

When I point my browser to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“ it shows up fine!  but when I edit the “bgcolor” from blue to orange and refresh my page, it remains blue.  It didn’t bother me at first so I went ahead and created a test database so I can begin adding my lab’s gff files to gbrowse.  But it didn’t show up when I pointed my browser to "http://localhost/cgi-bin/gb2/gbrowse/test/“, in fact, it redirected it back to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“.  So, I thinking that maybe the reason my volvox.conf didn’t change the color to orange was the same reason my test database didn’t work.  Where should I be looking to figure out the problem?

Thanks,
Matt

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Re: Problem With Custom Track Entries in the Uploads Table of the Users.SQLite Database

Cruncher
In reply to this post by Cruncher
I made some more progress on this. It looks like I had two problems:
  1. trackids need to be 32 bit hex, within gbrowse they are created like this: md5_hex($userid.$filename.$data_source)
  2. newly created custom tracks need to be added to an internal hash of user uploads called "track_lookup" to be displayed

I just need to figure out how to modify the track_lookup hash and I should have this working(I hope).


Thanks,

Brad



On Thu, Apr 10, 2014 at 1:20 PM, Brad Covey <[hidden email]> wrote:
After further testing I was able to narrow it down to a problem with the trackids that my script is creating. Is there some specific formatting that these IDs need to follow? Currently I'm just creating random 32 character alphanumeric strings.

Thanks,
Brad


On Thu, Apr 10, 2014 at 11:44 AM, Brad Covey <[hidden email]> wrote:
Hi Guys,

I'm uploading large files to GBrowse manually as custom tracks. I've written scripts to create the sqlite database for the upload, the proper folder structure under "userdata", and the entry in the users.sqlite database.

The directory structure that is created looks like this:
userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite  
                STATUS     
                feature_name.conf  
                SOURCES/
                    feature_name


The upload seems to work fine and the new track appears under "Custom Tracks" as shown in the following screenshot:
Inline image 1

here "might-have-fixed-the-featurefile" is the new upload.

But the upload is not shown under "Select Tracks":
Inline image 2

I've done a bit of troubleshooting to try to figure out why this is happening. I've narrowed the problem down to the entry in the "uploads" table of the "users.sqlite" database.
These are the current entries in the database:

"2","private","trying-again",                            "","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again",                            "0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile","0"

I included the "trying-again" entry as a working example for reference.
note: the trackid is 32 characters long for both


As far as I can tell there is no difference between the two entries, but if I point the working "trying-again" entry at the non-working "might-have-fixed-the-featurefile" path like so:

"2","private","might-have-fixed-the-featurefile","","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again showing might-have-fixed-the-featurefile","0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile",                               "0"

My initially non-working track is displayed properly:
Inline image 3

Which tells me that the folder structure, sqlite sqlite database, and configuration for my new custom track are being created properly but there is some problem with the entry in the "uploads" table of the users.sqlite database preventing the track from being displayed properly.


Does anyone have any idea what may be wrong with the "uploads" entries that my script is creating?


Thanks,
Brad




------------------------------------------------------------------------------
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Re: Problem With Custom Track Entries in the Uploads Table of the Users.SQLite Database

Cruncher
Hey guys,

I finally cracked it! My newly created custom tracks weren't being added to the track_lookup hash because the hash uses the configuration labels for the tracks as keys in the hash and all of the tracks being generated by my script were being given the same configuration label.

[expression]   <----- configuration label
feature = expression
glyph = xyplot


It looks like I have this figured out, at long last.

Thanks for all the help along the way,
Brad


On Fri, Apr 11, 2014 at 12:40 PM, Brad Covey <[hidden email]> wrote:
I made some more progress on this. It looks like I had two problems:
  1. trackids need to be 32 bit hex, within gbrowse they are created like this: md5_hex($userid.$filename.$data_source)
  2. newly created custom tracks need to be added to an internal hash of user uploads called "track_lookup" to be displayed

I just need to figure out how to modify the track_lookup hash and I should have this working(I hope).


Thanks,

Brad



On Thu, Apr 10, 2014 at 1:20 PM, Brad Covey <[hidden email]> wrote:
After further testing I was able to narrow it down to a problem with the trackids that my script is creating. Is there some specific formatting that these IDs need to follow? Currently I'm just creating random 32 character alphanumeric strings.

Thanks,
Brad


On Thu, Apr 10, 2014 at 11:44 AM, Brad Covey <[hidden email]> wrote:
Hi Guys,

I'm uploading large files to GBrowse manually as custom tracks. I've written scripts to create the sqlite database for the upload, the proper folder structure under "userdata", and the entry in the users.sqlite database.

The directory structure that is created looks like this:
userdata/
    datasource_name/
        user_uploadsid/
            feature_name/
                index.SQLite  
                STATUS     
                feature_name.conf  
                SOURCES/
                    feature_name


The upload seems to work fine and the new track appears under "Custom Tracks" as shown in the following screenshot:
Inline image 1

here "might-have-fixed-the-featurefile" is the new upload.

But the upload is not shown under "Select Tracks":
Inline image 2

I've done a bit of troubleshooting to try to figure out why this is happening. I've narrowed the problem down to the entry in the "uploads" table of the "users.sqlite" database.
These are the current entries in the database:

"2","private","trying-again",                            "","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again",                            "0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile","0"

I included the "trying-again" entry as a working example for reference.
note: the trackid is 32 characters long for both


As far as I can tell there is no difference between the two entries, but if I point the working "trying-again" entry at the non-working "might-have-fixed-the-featurefile" path like so:

"2","private","might-have-fixed-the-featurefile","","yoxphwmgxhjlzf3ngjk3ew5xbuwnoytl","Toceanica2","2014-04-08 16:24:11","2014-04-08 16:24:11","","trying-again showing might-have-fixed-the-featurefile","0"
"2","private","might-have-fixed-the-featurefile","","6c0yilb5r2yirwffht32ixg1tusdsjpk",      "Toceanica2","2014-04-10 10:42:03","2014-04-10 10:42:03","","might-have-fixed-the-featurefile",                               "0"

My initially non-working track is displayed properly:
Inline image 3

Which tells me that the folder structure, sqlite sqlite database, and configuration for my new custom track are being created properly but there is some problem with the entry in the "uploads" table of the users.sqlite database preventing the track from being displayed properly.


Does anyone have any idea what may be wrong with the "uploads" entries that my script is creating?


Thanks,
Brad





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volvox tutorial conf files

Matthew Johnson
In reply to this post by Matthew Johnson
Hey Guys,

I’ve started the tutorial and setup the volvox database and configured the gbrowse.conf to point to the volvox.conf.  The bottom of my volvox.conf reads:

[ExampleFeatures]
feature      = remark
glyph        = generic
stranded     = 1
bgcolor      = blue
height       = 10
key          = Example Features

When I point my browser to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“ it shows up fine!  but when I edit the “bgcolor” from blue to orange and refresh my page, it remains blue.  It didn’t bother me at first so I went ahead and created a test database so I can begin adding my lab’s gff files to gbrowse.  But it didn’t show up when I pointed my browser to "http://localhost/cgi-bin/gb2/gbrowse/test/“, in fact, it redirected it back to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“.  So, I thinking that maybe the reason my volvox.conf didn’t change the color to orange was the same reason my test database didn’t work.  Where should I be looking to figure out the problem?

Thanks,
Matt

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Re: volvox tutorial conf files

Scott Cain
In reply to this post by Matthew Johnson
Hi Matt,

Sorry I missed this last week: I was traveling and it fell through the cracks.

Generally, when you are editing the conf file and don't see the change there are a few reasons that are at the root of the problem:

1. You didn't really save the conf file (this is analogous to "is it plugged in"--it's a silly question right until you realize it's the reason :-)

2. You aren't actually editing the right conf file.  I've done this more than once, where there are multiple copies of the conf file spread around the file system.

3. Just hitting refresh doesn't cause GBrowse to recreate the image.  GBrowse is fairly conservative about drawing images and caches ones that it's made on the server.  If you make a request for exactly the same image (which is what you're doing when you hit refresh), GBrowse just hands back the image it already created.  Instead, you can do a few things to force GBrowse to redraw: zoom or pan to a different location (different by one bp will do it) or, in the preferences tab, hit the "update appearance" button, which forces GBrowse to reread the config file.

Now, for the test database, did you create an entry at the bottom of the GBrowse.conf file for it?

Scott



On Thu, Apr 10, 2014 at 2:51 PM, Matthew Johnson <[hidden email]> wrote:
Hey Guys,

I’ve started the tutorial and setup the volvox database and configured the gbrowse.conf to point to the volvox.conf.  The bottom of my volvox.conf reads:

[ExampleFeatures]
feature      = remark
glyph        = generic
stranded     = 1
bgcolor      = blue
height       = 10
key          = Example Features

When I point my browser to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“ it shows up fine!  but when I edit the “bgcolor” from blue to orange and refresh my page, it remains blue.  It didn’t bother me at first so I went ahead and created a test database so I can begin adding my lab’s gff files to gbrowse.  But it didn’t show up when I pointed my browser to "http://localhost/cgi-bin/gb2/gbrowse/test/“, in fact, it redirected it back to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“.  So, I thinking that maybe the reason my volvox.conf didn’t change the color to orange was the same reason my test database didn’t work.  Where should I be looking to figure out the problem?

Thanks,
Matt

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--
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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: volvox tutorial conf files

Matthew Johnson
Hey Scott,

No worries, I appreciate the help.

I verified that the conf files are saving the changes I make to them.  All of the conf files I am working with are located in my /etc/gbrowse2 folder.  I also noticed that for every conf file there are two files with the same name ending in .conf.new and .conf.orig.  Not sure if that came with the install but I haven’t touched those.   I tried editing the sample yeast conf files and neither did those change bgcolor. 

For the test database, I did put the entry at the bottom of the GBrowse.conf file.  I did it twice just to make sure I didn’t miss a step but it still didn’t work.

Best,
Matt

On Apr 17, 2014, at 5:09 PM, Scott Cain <[hidden email]> wrote:

Hi Matt,

Sorry I missed this last week: I was traveling and it fell through the cracks.

Generally, when you are editing the conf file and don't see the change there are a few reasons that are at the root of the problem:

1. You didn't really save the conf file (this is analogous to "is it plugged in"--it's a silly question right until you realize it's the reason :-)

2. You aren't actually editing the right conf file.  I've done this more than once, where there are multiple copies of the conf file spread around the file system.

3. Just hitting refresh doesn't cause GBrowse to recreate the image.  GBrowse is fairly conservative about drawing images and caches ones that it's made on the server.  If you make a request for exactly the same image (which is what you're doing when you hit refresh), GBrowse just hands back the image it already created.  Instead, you can do a few things to force GBrowse to redraw: zoom or pan to a different location (different by one bp will do it) or, in the preferences tab, hit the "update appearance" button, which forces GBrowse to reread the config file.

Now, for the test database, did you create an entry at the bottom of the GBrowse.conf file for it?

Scott



On Thu, Apr 10, 2014 at 2:51 PM, Matthew Johnson <[hidden email]> wrote:
Hey Guys,

I’ve started the tutorial and setup the volvox database and configured the gbrowse.conf to point to the volvox.conf.  The bottom of my volvox.conf reads:

[ExampleFeatures]
feature      = remark
glyph        = generic
stranded     = 1
bgcolor      = blue
height       = 10
key          = Example Features

When I point my browser to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“ it shows up fine!  but when I edit the “bgcolor” from blue to orange and refresh my page, it remains blue.  It didn’t bother me at first so I went ahead and created a test database so I can begin adding my lab’s gff files to gbrowse.  But it didn’t show up when I pointed my browser to "http://localhost/cgi-bin/gb2/gbrowse/test/“, in fact, it redirected it back to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“.  So, I thinking that maybe the reason my volvox.conf didn’t change the color to orange was the same reason my test database didn’t work.  Where should I be looking to figure out the problem?

Thanks,
Matt

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


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Re: volvox tutorial conf files

Scott Cain
Hi Matt,

You didn't mention the other items I pointed out about getting GBrowse to redraw images (zoom/panning/hitting "update appearance"). 

When you say that adding items to GBrowse.conf doesn't work, what do you mean?  They don't show up in the drop down list?  What if you comment something out, does that change anything?

One item I didn't mention is fastcgi; are you using that?  If so, you have to restart apache to get config file changes to be read.

If you've addressed all of these things, then I am really thinking your not editing the files that GBrowse is looking at.

Scott




On Thu, Apr 17, 2014 at 10:41 PM, Matthew Johnson <[hidden email]> wrote:
Hey Scott,

No worries, I appreciate the help.

I verified that the conf files are saving the changes I make to them.  All of the conf files I am working with are located in my /etc/gbrowse2 folder.  I also noticed that for every conf file there are two files with the same name ending in .conf.new and .conf.orig.  Not sure if that came with the install but I haven’t touched those.   I tried editing the sample yeast conf files and neither did those change bgcolor. 

For the test database, I did put the entry at the bottom of the GBrowse.conf file.  I did it twice just to make sure I didn’t miss a step but it still didn’t work.

Best,
Matt

On Apr 17, 2014, at 5:09 PM, Scott Cain <[hidden email]> wrote:

Hi Matt,

Sorry I missed this last week: I was traveling and it fell through the cracks.

Generally, when you are editing the conf file and don't see the change there are a few reasons that are at the root of the problem:

1. You didn't really save the conf file (this is analogous to "is it plugged in"--it's a silly question right until you realize it's the reason :-)

2. You aren't actually editing the right conf file.  I've done this more than once, where there are multiple copies of the conf file spread around the file system.

3. Just hitting refresh doesn't cause GBrowse to recreate the image.  GBrowse is fairly conservative about drawing images and caches ones that it's made on the server.  If you make a request for exactly the same image (which is what you're doing when you hit refresh), GBrowse just hands back the image it already created.  Instead, you can do a few things to force GBrowse to redraw: zoom or pan to a different location (different by one bp will do it) or, in the preferences tab, hit the "update appearance" button, which forces GBrowse to reread the config file.

Now, for the test database, did you create an entry at the bottom of the GBrowse.conf file for it?

Scott



On Thu, Apr 10, 2014 at 2:51 PM, Matthew Johnson <[hidden email]> wrote:
Hey Guys,

I’ve started the tutorial and setup the volvox database and configured the gbrowse.conf to point to the volvox.conf.  The bottom of my volvox.conf reads:

[ExampleFeatures]
feature      = remark
glyph        = generic
stranded     = 1
bgcolor      = blue
height       = 10
key          = Example Features

When I point my browser to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“ it shows up fine!  but when I edit the “bgcolor” from blue to orange and refresh my page, it remains blue.  It didn’t bother me at first so I went ahead and created a test database so I can begin adding my lab’s gff files to gbrowse.  But it didn’t show up when I pointed my browser to "http://localhost/cgi-bin/gb2/gbrowse/test/“, in fact, it redirected it back to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“.  So, I thinking that maybe the reason my volvox.conf didn’t change the color to orange was the same reason my test database didn’t work.  Where should I be looking to figure out the problem?

Thanks,
Matt

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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: volvox tutorial conf files

Matthew Johnson
Hey Scott,

I did a spotlight search to find all of the volvox conf files on my machine.  Turns out I had at least 5 copies located in different locations.  I was editing the ones in my /etc/gbrowse2 but the true location was in /opt/local/apache2/conf/gbrowse2/volvox.conf  edited that one and it did the trick!  I didn’t even notice the drop down menu allowed you to change databases. 

Thanks for the help!   I will now go about making a test database with the true location of the conf files.

Best,
Matt
On Apr 18, 2014, at 11:24 AM, Scott Cain <[hidden email]> wrote:

Hi Matt,

You didn't mention the other items I pointed out about getting GBrowse to redraw images (zoom/panning/hitting "update appearance"). 

When you say that adding items to GBrowse.conf doesn't work, what do you mean?  They don't show up in the drop down list?  What if you comment something out, does that change anything?

One item I didn't mention is fastcgi; are you using that?  If so, you have to restart apache to get config file changes to be read.

If you've addressed all of these things, then I am really thinking your not editing the files that GBrowse is looking at.

Scott




On Thu, Apr 17, 2014 at 10:41 PM, Matthew Johnson <[hidden email]> wrote:
Hey Scott,

No worries, I appreciate the help.

I verified that the conf files are saving the changes I make to them.  All of the conf files I am working with are located in my /etc/gbrowse2 folder.  I also noticed that for every conf file there are two files with the same name ending in .conf.new and .conf.orig.  Not sure if that came with the install but I haven’t touched those.   I tried editing the sample yeast conf files and neither did those change bgcolor. 

For the test database, I did put the entry at the bottom of the GBrowse.conf file.  I did it twice just to make sure I didn’t miss a step but it still didn’t work.

Best,
Matt

On Apr 17, 2014, at 5:09 PM, Scott Cain <[hidden email]> wrote:

Hi Matt,

Sorry I missed this last week: I was traveling and it fell through the cracks.

Generally, when you are editing the conf file and don't see the change there are a few reasons that are at the root of the problem:

1. You didn't really save the conf file (this is analogous to "is it plugged in"--it's a silly question right until you realize it's the reason :-)

2. You aren't actually editing the right conf file.  I've done this more than once, where there are multiple copies of the conf file spread around the file system.

3. Just hitting refresh doesn't cause GBrowse to recreate the image.  GBrowse is fairly conservative about drawing images and caches ones that it's made on the server.  If you make a request for exactly the same image (which is what you're doing when you hit refresh), GBrowse just hands back the image it already created.  Instead, you can do a few things to force GBrowse to redraw: zoom or pan to a different location (different by one bp will do it) or, in the preferences tab, hit the "update appearance" button, which forces GBrowse to reread the config file.

Now, for the test database, did you create an entry at the bottom of the GBrowse.conf file for it?

Scott



On Thu, Apr 10, 2014 at 2:51 PM, Matthew Johnson <[hidden email]> wrote:
Hey Guys,

I’ve started the tutorial and setup the volvox database and configured the gbrowse.conf to point to the volvox.conf.  The bottom of my volvox.conf reads:

[ExampleFeatures]
feature      = remark
glyph        = generic
stranded     = 1
bgcolor      = blue
height       = 10
key          = Example Features

When I point my browser to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“ it shows up fine!  but when I edit the “bgcolor” from blue to orange and refresh my page, it remains blue.  It didn’t bother me at first so I went ahead and created a test database so I can begin adding my lab’s gff files to gbrowse.  But it didn’t show up when I pointed my browser to "http://localhost/cgi-bin/gb2/gbrowse/test/“, in fact, it redirected it back to "http://localhost/cgi-bin/gb2/gbrowse/volvox/“.  So, I thinking that maybe the reason my volvox.conf didn’t change the color to orange was the same reason my test database didn’t work.  Where should I be looking to figure out the problem?

Thanks,
Matt

------------------------------------------------------------------------------
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Dominate Development with Jenkins Continuous Integration
Continuously Automate Build, Test & Deployment
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research


------------------------------------------------------------------------------
Learn Graph Databases - Download FREE O'Reilly Book
"Graph Databases" is the definitive new guide to graph databases and their
applications. Written by three acclaimed leaders in the field,
this first edition is now available. Download your free book today!
http://p.sf.net/sfu/NeoTech
_______________________________________________
Gmod-gbrowse mailing list
[hidden email]
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