Error 404 on WEB-INF/grails-app/views/jbrowse/data.gsp

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Error 404 on WEB-INF/grails-app/views/jbrowse/data.gsp

Heleen
Hi,

I am still testing and currently use the same volvox sample data in a JBrowse instance and in an Apollo instance.

When trying to display from the raw directory, ie. BAM other than legacy BAM it will give me an error on Apollo, but not in JBrowse.

The error is:
HTTP Status 404 - "/WEB-INF/grails-app/views/jbrowse/data.gsp" not found

If I test the same link with a random .html file it will display. If I test the .bam file via URL and it will give me the same error about data.gsp. So it does not appear to be a URL/path problem.

I did a search for data.gsp and it is not installed anywhere.

Did I miss something during the install?

Thanks!
Heleen.










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Re: Error 404 on WEB-INF/grails-app/views/jbrowse/data.gsp

nathandunn

Can you repeat the experiment with your javascript and network console in developer tools and copy the information in (at least the failures)?

My guess is that there is a suffix we haven’t accounted for in Apollo, but I can’t be sure.  

Thanks,

Nathan

> On Feb 28, 2017, at 6:56 AM, Heleen <[hidden email]> wrote:
>
> Hi,
>
> I am still testing and currently use the same volvox sample data in a JBrowse instance and in an Apollo instance.
>
> When trying to display from the raw directory, ie. BAM other than legacy BAM it will give me an error on Apollo, but not in JBrowse.
>
> The error is:
> HTTP Status 404 - "/WEB-INF/grails-app/views/jbrowse/data.gsp" not found
>
> If I test the same link with a random .html file it will display. If I test the .bam file via URL and it will give me the same error about data.gsp. So it does not appear to be a URL/path problem.
>
> I did a search for data.gsp and it is not installed anywhere.
>
> Did I miss something during the install?
>
> Thanks!
> Heleen.
>
>
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>




This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Error 404 on WEB-INF/grails-app/views/jbrowse/data.gsp

Heleen
Hi Nathan,

These are the errors from the browser.

Inline afbeelding 1

Also I am having a problem creating an organism for a directory with indexed fasta files. It will not accept the directory. It gives me an error but it goes away immediately, so I can't see what it says.

Thanks,
Heleen.


2017-02-28 17:55 GMT+01:00 Nathan Dunn <[hidden email]>:

Can you repeat the experiment with your javascript and network console in developer tools and copy the information in (at least the failures)?

My guess is that there is a suffix we haven’t accounted for in Apollo, but I can’t be sure.

Thanks,

Nathan

> On Feb 28, 2017, at 6:56 AM, Heleen <[hidden email]> wrote:
>
> Hi,
>
> I am still testing and currently use the same volvox sample data in a JBrowse instance and in an Apollo instance.
>
> When trying to display from the raw directory, ie. BAM other than legacy BAM it will give me an error on Apollo, but not in JBrowse.
>
> The error is:
> HTTP Status 404 - "/WEB-INF/grails-app/views/jbrowse/data.gsp" not found
>
> If I test the same link with a random .html file it will display. If I test the .bam file via URL and it will give me the same error about data.gsp. So it does not appear to be a URL/path problem.
>
> I did a search for data.gsp and it is not installed anywhere.
>
> Did I miss something during the install?
>
> Thanks!
> Heleen.
>
>
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Error 404 on WEB-INF/grails-app/views/jbrowse/data.gsp

nathandunn

You organism should point to a directory that has these contents, where everything but tracks.conf and trackList.json are directories:

names  raw  seq  trackList.json  tracks  tracks.conf

I put mine in a directory in /opt/ or /var/

Does it work for other data types, or does it just fail for bw files? 

I tested it on all of the bigwig files from the sample directory and they worked fine for me. 

Do you have any errors in the tomcat logs (typically catalina.out)?   


If you could provide me more details about the indexed fasta files (e.g., how you setup the directory for Apollo / JBrowse).  

Thanks,

Nathan

On Mar 1, 2017, at 8:05 AM, Heleen <[hidden email]> wrote:

Hi Nathan,

These are the errors from the browser.

<image.png>

Also I am having a problem creating an organism for a directory with indexed fasta files. It will not accept the directory. It gives me an error but it goes away immediately, so I can't see what it says.

Thanks,
Heleen.


2017-02-28 17:55 GMT+01:00 Nathan Dunn <[hidden email]>:

Can you repeat the experiment with your javascript and network console in developer tools and copy the information in (at least the failures)?

My guess is that there is a suffix we haven’t accounted for in Apollo, but I can’t be sure.

Thanks,

Nathan

> On Feb 28, 2017, at 6:56 AM, Heleen <[hidden email]> wrote:
>
> Hi,
>
> I am still testing and currently use the same volvox sample data in a JBrowse instance and in an Apollo instance.
>
> When trying to display from the raw directory, ie. BAM other than legacy BAM it will give me an error on Apollo, but not in JBrowse.
>
> The error is:
> HTTP Status 404 - "/WEB-INF/grails-app/views/jbrowse/data.gsp" not found
>
> If I test the same link with a random .html file it will display. If I test the .bam file via URL and it will give me the same error about data.gsp. So it does not appear to be a URL/path problem.
>
> I did a search for data.gsp and it is not installed anywhere.
>
> Did I miss something during the install?
>
> Thanks!
> Heleen.
>
>
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Error 404 on WEB-INF/grails-app/views/jbrowse/data.gsp

Heleen
Hi Nathan,

Thanks very much for your prompt response. I was using a JBrowse directory sample structure. It has another subdirectory called json and that was causing the problem. So all is working fine now I've moved the file structure as suggested.

I have tried to get the indexed fasta files to work, but so far no result. If I change the seq dir with "normal" sub-sub-dir chunks I can create an organism. If I subsequently change the seq dir with indexed fasta it will show ??? on the sequence track. The seq dir has 3 files: organism.fa, organism.fa.fai and refSeqs.json. As mentioned before, the same dir does work on JBrowse. It's not a major issue, I can just work with the standard fasta.

Thanks,
Heleen.


2017-03-01 20:29 GMT+01:00 Nathan Dunn <[hidden email]>:

You organism should point to a directory that has these contents, where everything but tracks.conf and trackList.json are directories:

names  raw  seq  trackList.json  tracks  tracks.conf

I put mine in a directory in /opt/ or /var/

Does it work for other data types, or does it just fail for bw files? 

I tested it on all of the bigwig files from the sample directory and they worked fine for me. 

Do you have any errors in the tomcat logs (typically catalina.out)?   


If you could provide me more details about the indexed fasta files (e.g., how you setup the directory for Apollo / JBrowse).  

Thanks,

Nathan

On Mar 1, 2017, at 8:05 AM, Heleen <[hidden email]> wrote:

Hi Nathan,

These are the errors from the browser.

<image.png>

Also I am having a problem creating an organism for a directory with indexed fasta files. It will not accept the directory. It gives me an error but it goes away immediately, so I can't see what it says.

Thanks,
Heleen.


2017-02-28 17:55 GMT+01:00 Nathan Dunn <[hidden email]>:

Can you repeat the experiment with your javascript and network console in developer tools and copy the information in (at least the failures)?

My guess is that there is a suffix we haven’t accounted for in Apollo, but I can’t be sure.

Thanks,

Nathan

> On Feb 28, 2017, at 6:56 AM, Heleen <[hidden email]> wrote:
>
> Hi,
>
> I am still testing and currently use the same volvox sample data in a JBrowse instance and in an Apollo instance.
>
> When trying to display from the raw directory, ie. BAM other than legacy BAM it will give me an error on Apollo, but not in JBrowse.
>
> The error is:
> HTTP Status 404 - "/WEB-INF/grails-app/views/jbrowse/data.gsp" not found
>
> If I test the same link with a random .html file it will display. If I test the .bam file via URL and it will give me the same error about data.gsp. So it does not appear to be a URL/path problem.
>
> I did a search for data.gsp and it is not installed anywhere.
>
> Did I miss something during the install?
>
> Thanks!
> Heleen.
>
>
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.







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If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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Re: Error 404 on WEB-INF/grails-app/views/jbrowse/data.gsp

nathandunn

Heleen,

That is correct.   It looks like we explored using it here: https://github.com/GMOD/Apollo/issues/517

but the branch it was on was not yet completed.    

I created a GH issue for it here:


If anyone is feeling ambitious, would love to see a PR for this ;) 

Nathan

On Mar 2, 2017, at 8:12 AM, Heleen <[hidden email]> wrote:

Hi Nathan,

Thanks very much for your prompt response. I was using a JBrowse directory sample structure. It has another subdirectory called json and that was causing the problem. So all is working fine now I've moved the file structure as suggested.

I have tried to get the indexed fasta files to work, but so far no result. If I change the seq dir with "normal" sub-sub-dir chunks I can create an organism. If I subsequently change the seq dir with indexed fasta it will show ??? on the sequence track. The seq dir has 3 files: organism.fa, organism.fa.fai and refSeqs.json. As mentioned before, the same dir does work on JBrowse. It's not a major issue, I can just work with the standard fasta.

Thanks,
Heleen.


2017-03-01 20:29 GMT+01:00 Nathan Dunn <[hidden email]>:

You organism should point to a directory that has these contents, where everything but tracks.conf and trackList.json are directories:

names  raw  seq  trackList.json  tracks  tracks.conf

I put mine in a directory in /opt/ or /var/

Does it work for other data types, or does it just fail for bw files? 

I tested it on all of the bigwig files from the sample directory and they worked fine for me. 

Do you have any errors in the tomcat logs (typically catalina.out)?   


If you could provide me more details about the indexed fasta files (e.g., how you setup the directory for Apollo / JBrowse).  

Thanks,

Nathan

On Mar 1, 2017, at 8:05 AM, Heleen <[hidden email]> wrote:

Hi Nathan,

These are the errors from the browser.

<image.png>

Also I am having a problem creating an organism for a directory with indexed fasta files. It will not accept the directory. It gives me an error but it goes away immediately, so I can't see what it says.

Thanks,
Heleen.


2017-02-28 17:55 GMT+01:00 Nathan Dunn <[hidden email]>:

Can you repeat the experiment with your javascript and network console in developer tools and copy the information in (at least the failures)?

My guess is that there is a suffix we haven’t accounted for in Apollo, but I can’t be sure.

Thanks,

Nathan

> On Feb 28, 2017, at 6:56 AM, Heleen <[hidden email]> wrote:
>
> Hi,
>
> I am still testing and currently use the same volvox sample data in a JBrowse instance and in an Apollo instance.
>
> When trying to display from the raw directory, ie. BAM other than legacy BAM it will give me an error on Apollo, but not in JBrowse.
>
> The error is:
> HTTP Status 404 - "/WEB-INF/grails-app/views/jbrowse/data.gsp" not found
>
> If I test the same link with a random .html file it will display. If I test the .bam file via URL and it will give me the same error about data.gsp. So it does not appear to be a URL/path problem.
>
> I did a search for data.gsp and it is not installed anywhere.
>
> Did I miss something during the install?
>
> Thanks!
> Heleen.
>
>
>
>
>
>
>
>
>
> This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
> If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.
>





This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.






This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with which you subscribed to the list, send a message to [hidden email] | 2. In the subject line of your email type: unsubscribe apollo | 3. Leave the message body blank.

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