JBrowse gene structure displaying problem

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JBrowse gene structure displaying problem

Pengcheng Yang

Hi InterMiners,

I encounter one problem when embedding JBrowse. The stand alone JBrowse could display the gene structure as expected (figure 1). But the embedded JBrowse displaying the gene structure as one line with exon and intron merged (figure 2).

The JBrowse configuration process is listed below:

##1 modify the following content in the file: /var/www/html/jbrowse/JBrowse-1.16.4/index.html

<div class="jbrowse" id="GenomeBrowser" data-config='"allowCrossOriginDataRoot": true, "cacheBuster": true'>

 

##2. configure InterMine

##2.1 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/webconfig-model.xml

 

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"

                     jspName="model/jbrowseDisplayer.jsp"

                     replacesFields=""

                     placement="Genomics"

                     types="SequenceFeature"/>

 

##2.2 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/resources/model.properties

jbrowse.install.url = http://locustmine.org/jbrowse/JBrowse-1.16.4

 

##2.3 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/web.properties

org.intermine.webservice.server.jbrowse.genomic.track.Gene.class=Gene

org.intermine.webservice.server.jbrowse.genomic.track.CDS.class=CDS

org.intermine.webservice.server.jbrowse.genomic.track.Transcript.class=Transcript


Thank you and best,

Pengcheng Yang


figure 1. from stand alone JBrowse.

figure 2. from embedded JBrowse



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Re: JBrowse gene structure displaying problem

Pengcheng Yang

Hi,

I have tested whether the JBrowse could load the dataset from LocustMine through the link (http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://locustmine.org:8080/locustmine/query/service/jbrowse/config/7004) and failed. However, the test for flymine (http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://www.flymine.org/query/service/jbrowse/config/7227) succeed.

The failure testing for LocustMine gives error message said:

Error message(s):


Thank you and best,

Pengcheng Yang


On 2019-5-29 17:15, Pengcheng Yang wrote:

Hi InterMiners,

I encounter one problem when embedding JBrowse. The stand alone JBrowse could display the gene structure as expected (figure 1). But the embedded JBrowse displaying the gene structure as one line with exon and intron merged (figure 2).

The JBrowse configuration process is listed below:

##1 modify the following content in the file: /var/www/html/jbrowse/JBrowse-1.16.4/index.html

<div class="jbrowse" id="GenomeBrowser" data-config='"allowCrossOriginDataRoot": true, "cacheBuster": true'>

 

##2. configure InterMine

##2.1 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/webconfig-model.xml

 

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"

                     jspName="model/jbrowseDisplayer.jsp"

                     replacesFields=""

                     placement="Genomics"

                     types="SequenceFeature"/>

 

##2.2 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/resources/model.properties

jbrowse.install.url = http://locustmine.org/jbrowse/JBrowse-1.16.4

 

##2.3 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/web.properties

org.intermine.webservice.server.jbrowse.genomic.track.Gene.class=Gene

org.intermine.webservice.server.jbrowse.genomic.track.CDS.class=CDS

org.intermine.webservice.server.jbrowse.genomic.track.Transcript.class=Transcript


Thank you and best,

Pengcheng Yang


figure 1. from stand alone JBrowse.

figure 2. from embedded JBrowse



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Re: JBrowse gene structure displaying problem

Colin
Hi there (JBrowse dev here)

Status 0 errors are generally "CORS errors", you can see the javascript console for more info, you would have to fix your tomcat server to allow CORS or something like this.

For the gene structure, you might look into "inferCdsParts", this was contributed by Vivek Krishnakumar I believe for jbrowse tracks connecting to intermine instances

-Colin

On Wed, May 29, 2019 at 12:27 PM Pengcheng Yang <[hidden email]> wrote:

Hi,

I have tested whether the JBrowse could load the dataset from LocustMine through the link (http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://locustmine.org:8080/locustmine/query/service/jbrowse/config/7004) and failed. However, the test for flymine (http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://www.flymine.org/query/service/jbrowse/config/7227) succeed.

The failure testing for LocustMine gives error message said:

Error message(s):


Thank you and best,

Pengcheng Yang


On 2019-5-29 17:15, Pengcheng Yang wrote:

Hi InterMiners,

I encounter one problem when embedding JBrowse. The stand alone JBrowse could display the gene structure as expected (figure 1). But the embedded JBrowse displaying the gene structure as one line with exon and intron merged (figure 2).

The JBrowse configuration process is listed below:

##1 modify the following content in the file: /var/www/html/jbrowse/JBrowse-1.16.4/index.html

<div class="jbrowse" id="GenomeBrowser" data-config='"allowCrossOriginDataRoot": true, "cacheBuster": true'>

 

##2. configure InterMine

##2.1 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/webconfig-model.xml

 

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"

                     jspName="model/jbrowseDisplayer.jsp"

                     replacesFields=""

                     placement="Genomics"

                     types="SequenceFeature"/>

 

##2.2 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/resources/model.properties

jbrowse.install.url = http://locustmine.org/jbrowse/JBrowse-1.16.4

 

##2.3 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/web.properties

org.intermine.webservice.server.jbrowse.genomic.track.Gene.class=Gene

org.intermine.webservice.server.jbrowse.genomic.track.CDS.class=CDS

org.intermine.webservice.server.jbrowse.genomic.track.Transcript.class=Transcript


Thank you and best,

Pengcheng Yang


figure 1. from stand alone JBrowse.

figure 2. from embedded JBrowse



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Re: JBrowse gene structure displaying problem

Pengcheng Yang

Hi Colin,

Thank you for your information.

According to your suggestion, I have tested the following steps:

1. CORS configuration

##after adding the following content to the file: /home/pengchy/soft/apache-tomcat-8.5.30/conf/web.xml, the LocustMine embedded JBrowse displaying collapsed.

  <filter>
    <filter-name>CorsFilter</filter-name>
    <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
  </filter>
  <filter-mapping>
    <filter-name>CorsFilter</filter-name>
    <url-pattern>/*</url-pattern>
  </filter-mapping>

The embedded JBrowse returned the error message said:


The http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://locustmine.org:8080/locustmine/query/service/jbrowse/config/7004
returned error message said:

2. "inferCdsParts" configuration

## add the following content to the file: webapp/src/main/webapp/WEB-INF/web.properties

org.intermine.webservice.server.jbrowse.genomic.track.Gene.inferCdsParts=false

or

org.intermine.webservice.server.jbrowse.genomic.track.Gene.inferCdsParts=true

Both true or false could not change the displaying that a single CDS span covering the whole gene.

Best,

Pengcheng



On 2019-5-30 0:35, Colin wrote:
Hi there (JBrowse dev here)

Status 0 errors are generally "CORS errors", you can see the javascript console for more info, you would have to fix your tomcat server to allow CORS or something like this.

For the gene structure, you might look into "inferCdsParts", this was contributed by Vivek Krishnakumar I believe for jbrowse tracks connecting to intermine instances

-Colin

On Wed, May 29, 2019 at 12:27 PM Pengcheng Yang <[hidden email]> wrote:

Hi,

I have tested whether the JBrowse could load the dataset from LocustMine through the link (http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://locustmine.org:8080/locustmine/query/service/jbrowse/config/7004) and failed. However, the test for flymine (http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://www.flymine.org/query/service/jbrowse/config/7227) succeed.

The failure testing for LocustMine gives error message said:

Error message(s):


Thank you and best,

Pengcheng Yang


On 2019-5-29 17:15, Pengcheng Yang wrote:

Hi InterMiners,

I encounter one problem when embedding JBrowse. The stand alone JBrowse could display the gene structure as expected (figure 1). But the embedded JBrowse displaying the gene structure as one line with exon and intron merged (figure 2).

The JBrowse configuration process is listed below:

##1 modify the following content in the file: /var/www/html/jbrowse/JBrowse-1.16.4/index.html

<div class="jbrowse" id="GenomeBrowser" data-config='"allowCrossOriginDataRoot": true, "cacheBuster": true'>

 

##2. configure InterMine

##2.1 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/webconfig-model.xml

 

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"

                     jspName="model/jbrowseDisplayer.jsp"

                     replacesFields=""

                     placement="Genomics"

                     types="SequenceFeature"/>

 

##2.2 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/resources/model.properties

jbrowse.install.url = http://locustmine.org/jbrowse/JBrowse-1.16.4

 

##2.3 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/web.properties

org.intermine.webservice.server.jbrowse.genomic.track.Gene.class=Gene

org.intermine.webservice.server.jbrowse.genomic.track.CDS.class=CDS

org.intermine.webservice.server.jbrowse.genomic.track.Transcript.class=Transcript


Thank you and best,

Pengcheng Yang


figure 1. from stand alone JBrowse.

figure 2. from embedded JBrowse



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Re: JBrowse gene structure displaying problem

Colin
Here's a couple general tips. It's hard to navigate all the things going on here as (a) I'm not an intermine dev, just an observer and (b) lot of moving parts but here is my assesment

The cors error is due to requesting from locustmine.org to locustmine.org:8080 (e.g. the different port). if you just reverse proxied the tomcat onto port 80, you would not have a cors error, and also URLs look nicer without the port in them anyways

The issue you have with gene structure is due to how jbrowse is retrieving data from the intermine service. If you strongly want the jbrowse track to come from the intermine data service then you can press on, but clearly you have also loaded your jbrowse with the data you need already, so maybe you do not need this. In that case, consider embedding the jbrowse widget on your page without fetching the track from the intermine service.

-Colin

On Wed, May 29, 2019 at 11:32 PM Pengcheng Yang <[hidden email]> wrote:

Hi Colin,

Thank you for your information.

According to your suggestion, I have tested the following steps:

1. CORS configuration

##after adding the following content to the file: /home/pengchy/soft/apache-tomcat-8.5.30/conf/web.xml, the LocustMine embedded JBrowse displaying collapsed.

  <filter>
    <filter-name>CorsFilter</filter-name>
    <filter-class>org.apache.catalina.filters.CorsFilter</filter-class>
  </filter>
  <filter-mapping>
    <filter-name>CorsFilter</filter-name>
    <url-pattern>/*</url-pattern>
  </filter-mapping>

The embedded JBrowse returned the error message said:


The http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://locustmine.org:8080/locustmine/query/service/jbrowse/config/7004
returned error message said:

2. "inferCdsParts" configuration

## add the following content to the file: webapp/src/main/webapp/WEB-INF/web.properties

org.intermine.webservice.server.jbrowse.genomic.track.Gene.inferCdsParts=false

or

org.intermine.webservice.server.jbrowse.genomic.track.Gene.inferCdsParts=true

Both true or false could not change the displaying that a single CDS span covering the whole gene.

Best,

Pengcheng



On 2019-5-30 0:35, Colin wrote:
Hi there (JBrowse dev here)

Status 0 errors are generally "CORS errors", you can see the javascript console for more info, you would have to fix your tomcat server to allow CORS or something like this.

For the gene structure, you might look into "inferCdsParts", this was contributed by Vivek Krishnakumar I believe for jbrowse tracks connecting to intermine instances

-Colin

On Wed, May 29, 2019 at 12:27 PM Pengcheng Yang <[hidden email]> wrote:

Hi,

I have tested whether the JBrowse could load the dataset from LocustMine through the link (http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://locustmine.org:8080/locustmine/query/service/jbrowse/config/7004) and failed. However, the test for flymine (http://locustmine.org/jbrowse/JBrowse-1.16.4/?data=http://www.flymine.org/query/service/jbrowse/config/7227) succeed.

The failure testing for LocustMine gives error message said:

Error message(s):


Thank you and best,

Pengcheng Yang


On 2019-5-29 17:15, Pengcheng Yang wrote:

Hi InterMiners,

I encounter one problem when embedding JBrowse. The stand alone JBrowse could display the gene structure as expected (figure 1). But the embedded JBrowse displaying the gene structure as one line with exon and intron merged (figure 2).

The JBrowse configuration process is listed below:

##1 modify the following content in the file: /var/www/html/jbrowse/JBrowse-1.16.4/index.html

<div class="jbrowse" id="GenomeBrowser" data-config='"allowCrossOriginDataRoot": true, "cacheBuster": true'>

 

##2. configure InterMine

##2.1 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/webconfig-model.xml

 

    <reportdisplayer javaClass="org.intermine.bio.web.displayer.JBrowseDisplayer"

                     jspName="model/jbrowseDisplayer.jsp"

                     replacesFields=""

                     placement="Genomics"

                     types="SequenceFeature"/>

 

##2.2 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/resources/model.properties

jbrowse.install.url = http://locustmine.org/jbrowse/JBrowse-1.16.4

 

##2.3 add the following content to the file: /home/pengchy/soft/intermine.4.0/git/locustmine/webapp/src/main/webapp/WEB-INF/web.properties

org.intermine.webservice.server.jbrowse.genomic.track.Gene.class=Gene

org.intermine.webservice.server.jbrowse.genomic.track.CDS.class=CDS

org.intermine.webservice.server.jbrowse.genomic.track.Transcript.class=Transcript


Thank you and best,

Pengcheng Yang


figure 1. from stand alone JBrowse.

figure 2. from embedded JBrowse



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