region search configuration: Invalid property name 'strandSpecific'

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

region search configuration: Invalid property name 'strandSpecific'

Pengcheng Yang
Hi Interminers,

Following the documentation of region search
(http://intermine.readthedocs.io/en/latest/webapp/region-search/). I
have encountered an error output from catalina.out as follows.

1. the error message from catalina.out

767643 [http-apr-10.4.0.17-8080-exec-54] INFO
org.intermine.bio.web.logic.GenomicRegionSearchService  - REGION SEARCH
INIT total time: 0ms - getChromosomeInfomationMap: 0ms,
getFeatureTypesForOrgs: 0ms, getFeatureTypeToSOTermMap: 0ms,
getOrganismToTaxonMap: 0ms.
781077 [http-apr-10.4.0.17-8080-exec-60] ERROR
org.intermine.web.struts.InterMineExceptionHandler  -
java.lang.IllegalArgumentException: Invalid property name 'strandSpecific'
         at
org.apache.struts.action.DynaActionForm.getDynaProperty(DynaActionForm.java:638)
         at
org.apache.struts.action.DynaActionForm.get(DynaActionForm.java:236)
         at
org.intermine.bio.web.logic.GenomicRegionSearchService.parseBasicInput(GenomicRegionSearchService.java:499)
         at
org.intermine.bio.web.logic.GenomicRegionSearchService.parseGenomicRegionSearchForm(GenomicRegionSearchService.java:475)
         at
org.intermine.bio.web.struts.GenomicRegionSearchAction.execute(GenomicRegionSearchAction.java:70)
         at
org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
         at
org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
         at
org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
         at
org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:462)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
         at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
         at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
         at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
         at
org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
         at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
         at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
         at
org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
         at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
         at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
         at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
         at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
         at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
         at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
         at
org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
         at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
         at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
         at
org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
         at
org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
         at
org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
         at
org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
         at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
         at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
         at
org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
         at java.lang.Thread.run(Thread.java:748)

2. According to the error message, I have tested to 1) set
genomicRegionSearch.enableStrandSpecificSearch = false in web.properties
file;

2) I comment the following lines in
apache-tomcat-7.0.85/webapps/testmine/model/genomicRegionSearchOptionsBase.jsp
file.

                     <c:if
test="${WEB_PROPERTIES['genomicRegionSearch.enableStrandSpecificSearch']}">
                         <li id="genomicRegionStrandSpecific">
                             <html:checkbox property="strandSpecific"
value="true" />
                             <span>Check this box to perform a
strand-specific region search (search <b>+</b> strand if region
start&lt;end; search <b>&ndash;</b> strand if region end&lt;start)</span>
                         </li>
                     </c:if>

However, the error remains.

Could someone help me out?

Best,

Pengcheng Yang

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: region search configuration: Invalid property name 'strandSpecific'

Pengcheng Yang

Hi Interminers,

I have removed the error by setting the genomicRegionSearch.enableStrandSpecificSearch = true. I previously set this to false.

However, when I input three regions that indeed overlap with genes, the output was "No overlap features found", as following picture displayed. But there indeed overlapped genes in these regions. Could someone help me detect the reason?

Best,

Pengcheng


On 2018-4-27 22:49, Pengcheng Yang wrote:
Hi Interminers,

Following the documentation of region search (http://intermine.readthedocs.io/en/latest/webapp/region-search/). I have encountered an error output from catalina.out as follows.

1. the error message from catalina.out

767643 [http-apr-10.4.0.17-8080-exec-54] INFO org.intermine.bio.web.logic.GenomicRegionSearchService  - REGION SEARCH INIT total time: 0ms - getChromosomeInfomationMap: 0ms, getFeatureTypesForOrgs: 0ms, getFeatureTypeToSOTermMap: 0ms, getOrganismToTaxonMap: 0ms.
781077 [http-apr-10.4.0.17-8080-exec-60] ERROR org.intermine.web.struts.InterMineExceptionHandler  - java.lang.IllegalArgumentException: Invalid property name 'strandSpecific'
        at org.apache.struts.action.DynaActionForm.getDynaProperty(DynaActionForm.java:638)
        at org.apache.struts.action.DynaActionForm.get(DynaActionForm.java:236)
        at org.intermine.bio.web.logic.GenomicRegionSearchService.parseBasicInput(GenomicRegionSearchService.java:499)
        at org.intermine.bio.web.logic.GenomicRegionSearchService.parseGenomicRegionSearchForm(GenomicRegionSearchService.java:475)
        at org.intermine.bio.web.struts.GenomicRegionSearchAction.execute(GenomicRegionSearchAction.java:70)
        at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
        at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
        at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
        at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:462)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
        at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
        at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:748)

2. According to the error message, I have tested to 1) set genomicRegionSearch.enableStrandSpecificSearch = false in web.properties file;

2) I comment the following lines in apache-tomcat-7.0.85/webapps/testmine/model/genomicRegionSearchOptionsBase.jsp file.

                    <c:if test="${WEB_PROPERTIES['genomicRegionSearch.enableStrandSpecificSearch']}">
                        <li id="genomicRegionStrandSpecific">
                            <html:checkbox property="strandSpecific" value="true" />
                            <span>Check this box to perform a strand-specific region search (search <b>+</b> strand if region start&lt;end; search <b>&ndash;</b> strand if region end&lt;start)</span>
                        </li>
                    </c:if>

However, the error remains.

Could someone help me out?

Best,

Pengcheng Yang

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: region search configuration: Invalid property name 'strandSpecific'

Julie Sullivan-2
Hi Pengcheng,

What happens when you run the overlapping query in the query builder
with one of those regions. Do you see results?

What about if you look at that gene. Does it have overlapping features
on its report page?

Julie

On 04/27/2018 04:54 PM, Pengcheng Yang wrote:

> Hi Interminers,
>
> I have removed the error by setting the
> genomicRegionSearch.enableStrandSpecificSearch = true. I previously set
> this to false.
>
> However, when I input three regions that indeed overlap with genes, the
> output was "No overlap features found", as following picture displayed.
> But there indeed overlapped genes in these regions. Could someone help
> me detect the reason?
>
> Best,
>
> Pengcheng
>
>
> On 2018-4-27 22:49, Pengcheng Yang wrote:
>> Hi Interminers,
>>
>> Following the documentation of region search
>> (http://intermine.readthedocs.io/en/latest/webapp/region-search/). I
>> have encountered an error output from catalina.out as follows.
>>
>> 1. the error message from catalina.out
>>
>> 767643 [http-apr-10.4.0.17-8080-exec-54] INFO
>> org.intermine.bio.web.logic.GenomicRegionSearchService  - REGION
>> SEARCH INIT total time: 0ms - getChromosomeInfomationMap: 0ms,
>> getFeatureTypesForOrgs: 0ms, getFeatureTypeToSOTermMap: 0ms,
>> getOrganismToTaxonMap: 0ms.
>> 781077 [http-apr-10.4.0.17-8080-exec-60] ERROR
>> org.intermine.web.struts.InterMineExceptionHandler  -
>> java.lang.IllegalArgumentException: Invalid property name
>> 'strandSpecific'
>>         at
>> org.apache.struts.action.DynaActionForm.getDynaProperty(DynaActionForm.java:638)
>>         at
>> org.apache.struts.action.DynaActionForm.get(DynaActionForm.java:236)
>>         at
>> org.intermine.bio.web.logic.GenomicRegionSearchService.parseBasicInput(GenomicRegionSearchService.java:499)
>>         at
>> org.intermine.bio.web.logic.GenomicRegionSearchService.parseGenomicRegionSearchForm(GenomicRegionSearchService.java:475)
>>         at
>> org.intermine.bio.web.struts.GenomicRegionSearchAction.execute(GenomicRegionSearchAction.java:70)
>>         at
>> org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
>>         at
>> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
>>         at
>> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>         at
>> org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:462)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>         at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>         at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>         at
>> org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>         at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>         at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>         at
>> org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>>         at
>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>         at
>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>         at
>> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
>>         at
>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
>>         at
>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
>>         at
>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>         at
>> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
>>         at
>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>         at
>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
>>         at
>> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
>>         at
>> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
>>         at
>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
>>         at
>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
>>         at
>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>         at
>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>         at
>> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>         at java.lang.Thread.run(Thread.java:748)
>>
>> 2. According to the error message, I have tested to 1) set
>> genomicRegionSearch.enableStrandSpecificSearch = false in
>> web.properties file;
>>
>> 2) I comment the following lines in
>> apache-tomcat-7.0.85/webapps/testmine/model/genomicRegionSearchOptionsBase.jsp
>> file.
>>
>>                     <c:if
>> test="${WEB_PROPERTIES['genomicRegionSearch.enableStrandSpecificSearch']}">
>>                         <li id="genomicRegionStrandSpecific">
>>                             <html:checkbox property="strandSpecific"
>> value="true" />
>>                             <span>Check this box to perform a
>> strand-specific region search (search <b>+</b> strand if region
>> start&lt;end; search <b>&ndash;</b> strand if region end&lt;start)</span>
>>                         </li>
>>                     </c:if>
>>
>> However, the error remains.
>>
>> Could someone help me out?
>>
>> Best,
>>
>> Pengcheng Yang
>>
>> _______________________________________________
>> dev mailing list
>> [hidden email]
>> https://lists.intermine.org/mailman/listinfo/dev
>
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> https://lists.intermine.org/mailman/listinfo/dev
>
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: region search configuration: Invalid property name 'strandSpecific'

Sam Hokin-3
Reply | Threaded
Open this post in threaded view
|

Re: region search configuration: Invalid property name 'strandSpecific'

Pengcheng Yang
In reply to this post by Julie Sullivan-2

Hi Julie,

When I query using [1], the results as expected, returned 70 rows of location regions. The expected genes indeed were covered by this regions. I have checked the data model of the Location [2], which does not contain the "primaryIdentifier" or "identifier" attribute, could this be the reason?


[1] The query builder for region search

<query name="" model="genomic" view="Chromosome.primaryIdentifier Chromosome.locatedFeatures.start Chromosome.locatedFeatures.end" longDescription="" sortOrder="Chromosome.locatedFeatures.start asc" constraintLogic="A and B and C">
  <constraint path="Chromosome.primaryIdentifier" code="A" op="==" value="scaffold4976"/>
  <constraint path="Chromosome.locatedFeatures.start" code="B" op="&gt;" value="30000"/>
  <constraint path="Chromosome.locatedFeatures.start" code="C" op="&lt;" value="1410112"/>
</query>

[2] The data model of Location.

  <class name="Location" is-interface="true">
    <attribute name="start" type="java.lang.Integer"/>
    <attribute name="end" type="java.lang.Integer"/>
    <attribute name="strand" type="java.lang.String"/>
    <reference name="feature" referenced-type="BioEntity" reverse-reference="locations"/>
    <reference name="locatedOn" referenced-type="BioEntity" reverse-reference="locatedFeatures"/>
    <collection name="dataSets" referenced-type="DataSet"/>
  </class>

Thank you and best,
Pengcheng

On 2018-4-30 16:54, Julie Sullivan wrote:
Hi Pengcheng,

What happens when you run the overlapping query in the query builder with one of those regions. Do you see results?

What about if you look at that gene. Does it have overlapping features on its report page?

Julie

On 04/27/2018 04:54 PM, Pengcheng Yang wrote:
Hi Interminers,

I have removed the error by setting the genomicRegionSearch.enableStrandSpecificSearch = true. I previously set this to false.

However, when I input three regions that indeed overlap with genes, the output was "No overlap features found", as following picture displayed. But there indeed overlapped genes in these regions. Could someone help me detect the reason?

Best,

Pengcheng


On 2018-4-27 22:49, Pengcheng Yang wrote:
Hi Interminers,

Following the documentation of region search (http://intermine.readthedocs.io/en/latest/webapp/region-search/). I have encountered an error output from catalina.out as follows.

1. the error message from catalina.out

767643 [http-apr-10.4.0.17-8080-exec-54] INFO org.intermine.bio.web.logic.GenomicRegionSearchService  - REGION SEARCH INIT total time: 0ms - getChromosomeInfomationMap: 0ms, getFeatureTypesForOrgs: 0ms, getFeatureTypeToSOTermMap: 0ms, getOrganismToTaxonMap: 0ms.
781077 [http-apr-10.4.0.17-8080-exec-60] ERROR org.intermine.web.struts.InterMineExceptionHandler  - java.lang.IllegalArgumentException: Invalid property name 'strandSpecific'
        at org.apache.struts.action.DynaActionForm.getDynaProperty(DynaActionForm.java:638)
        at org.apache.struts.action.DynaActionForm.get(DynaActionForm.java:236)
        at org.intermine.bio.web.logic.GenomicRegionSearchService.parseBasicInput(GenomicRegionSearchService.java:499)
        at org.intermine.bio.web.logic.GenomicRegionSearchService.parseGenomicRegionSearchForm(GenomicRegionSearchService.java:475)
        at org.intermine.bio.web.struts.GenomicRegionSearchAction.execute(GenomicRegionSearchAction.java:70)
        at org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
        at org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
        at org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
        at org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:462)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
        at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
        at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
        at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
        at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
        at org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
        at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
        at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
        at org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
        at org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
        at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
        at org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
        at java.lang.Thread.run(Thread.java:748)

2. According to the error message, I have tested to 1) set genomicRegionSearch.enableStrandSpecificSearch = false in web.properties file;

2) I comment the following lines in apache-tomcat-7.0.85/webapps/testmine/model/genomicRegionSearchOptionsBase.jsp file.

                    <c:if test="${WEB_PROPERTIES['genomicRegionSearch.enableStrandSpecificSearch']}">
                        <li id="genomicRegionStrandSpecific">
                            <html:checkbox property="strandSpecific" value="true" />
                            <span>Check this box to perform a strand-specific region search (search <b>+</b> strand if region start&lt;end; search <b>&ndash;</b> strand if region end&lt;start)</span>
                        </li>
                    </c:if>

However, the error remains.

Could someone help me out?

Best,

Pengcheng Yang

_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev



_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev




_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: region search configuration: Invalid property name 'strandSpecific'

Julie Sullivan-2
Yes, that's the issue! Chromosome.locatedFeatures.feature is empty for
that query.

You have locations "locatedOn" on your chromosomes but those are not
associated with genes -- "feature" is empty. So the region search can't
retrieve them.


On 05/01/2018 10:06 AM, Pengcheng Yang wrote:

> Hi Julie,
>
> When I query using [1], the results as expected, returned 70 rows of
> location regions. The expected genes indeed were covered by this
> regions. I have checked the data model of the Location [2], which does
> not contain the "primaryIdentifier" or "identifier" attribute, could
> this be the reason?
>
>
> [1] The query builder for region search
>
> <query name="" model="genomic" view="Chromosome.primaryIdentifier Chromosome.locatedFeatures.start Chromosome.locatedFeatures.end" longDescription="" sortOrder="Chromosome.locatedFeatures.start asc" constraintLogic="A and B and C">
>    <constraint path="Chromosome.primaryIdentifier" code="A" op="==" value="scaffold4976"/>
>    <constraint path="Chromosome.locatedFeatures.start" code="B" op="&gt;" value="30000"/>
>    <constraint path="Chromosome.locatedFeatures.start" code="C" op="&lt;" value="1410112"/>
> </query>
>
> [2] The data model of Location.
>
>    <class name="Location" is-interface="true">
>      <attribute name="start" type="java.lang.Integer"/>
>      <attribute name="end" type="java.lang.Integer"/>
>      <attribute name="strand" type="java.lang.String"/>
>      <reference name="feature" referenced-type="BioEntity" reverse-reference="locations"/>
>      <reference name="locatedOn" referenced-type="BioEntity" reverse-reference="locatedFeatures"/>
>      <collection name="dataSets" referenced-type="DataSet"/>
>    </class>
>
> Thank you and best,
> Pengcheng
>
>
> On 2018-4-30 16:54, Julie Sullivan wrote:
>> Hi Pengcheng,
>>
>> What happens when you run the overlapping query in the query builder
>> with one of those regions. Do you see results?
>>
>> What about if you look at that gene. Does it have overlapping features
>> on its report page?
>>
>> Julie
>>
>> On 04/27/2018 04:54 PM, Pengcheng Yang wrote:
>>> Hi Interminers,
>>>
>>> I have removed the error by setting the
>>> genomicRegionSearch.enableStrandSpecificSearch = true. I previously
>>> set this to false.
>>>
>>> However, when I input three regions that indeed overlap with genes,
>>> the output was "No overlap features found", as following picture
>>> displayed. But there indeed overlapped genes in these regions. Could
>>> someone help me detect the reason?
>>>
>>> Best,
>>>
>>> Pengcheng
>>>
>>>
>>> On 2018-4-27 22:49, Pengcheng Yang wrote:
>>>> Hi Interminers,
>>>>
>>>> Following the documentation of region search
>>>> (http://intermine.readthedocs.io/en/latest/webapp/region-search/). I
>>>> have encountered an error output from catalina.out as follows.
>>>>
>>>> 1. the error message from catalina.out
>>>>
>>>> 767643 [http-apr-10.4.0.17-8080-exec-54] INFO
>>>> org.intermine.bio.web.logic.GenomicRegionSearchService  - REGION
>>>> SEARCH INIT total time: 0ms - getChromosomeInfomationMap: 0ms,
>>>> getFeatureTypesForOrgs: 0ms, getFeatureTypeToSOTermMap: 0ms,
>>>> getOrganismToTaxonMap: 0ms.
>>>> 781077 [http-apr-10.4.0.17-8080-exec-60] ERROR
>>>> org.intermine.web.struts.InterMineExceptionHandler  -
>>>> java.lang.IllegalArgumentException: Invalid property name
>>>> 'strandSpecific'
>>>>         at
>>>> org.apache.struts.action.DynaActionForm.getDynaProperty(DynaActionForm.java:638)
>>>>         at
>>>> org.apache.struts.action.DynaActionForm.get(DynaActionForm.java:236)
>>>>         at
>>>> org.intermine.bio.web.logic.GenomicRegionSearchService.parseBasicInput(GenomicRegionSearchService.java:499)
>>>>         at
>>>> org.intermine.bio.web.logic.GenomicRegionSearchService.parseGenomicRegionSearchForm(GenomicRegionSearchService.java:475)
>>>>         at
>>>> org.intermine.bio.web.struts.GenomicRegionSearchAction.execute(GenomicRegionSearchAction.java:70)
>>>>         at
>>>> org.apache.struts.action.RequestProcessor.processActionPerform(RequestProcessor.java:425)
>>>>         at
>>>> org.apache.struts.action.RequestProcessor.process(RequestProcessor.java:228)
>>>>         at
>>>> org.apache.struts.action.ActionServlet.process(ActionServlet.java:1913)
>>>>         at
>>>> org.apache.struts.action.ActionServlet.doPost(ActionServlet.java:462)
>>>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:650)
>>>>         at javax.servlet.http.HttpServlet.service(HttpServlet.java:731)
>>>>         at
>>>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)
>>>>         at
>>>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>         at
>>>> org.apache.tomcat.websocket.server.WsFilter.doFilter(WsFilter.java:52)
>>>>         at
>>>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>         at
>>>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>         at
>>>> org.intermine.web.filters.SetCharacterEncodingFilter.doFilter(SetCharacterEncodingFilter.java:139)
>>>>         at
>>>> org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:241)
>>>>         at
>>>> org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)
>>>>         at
>>>> org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)
>>>>         at
>>>> org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:110)
>>>>         at
>>>> org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:169)
>>>>         at
>>>> org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:103)
>>>>         at
>>>> org.apache.catalina.valves.AccessLogValve.invoke(AccessLogValve.java:962)
>>>>         at
>>>> org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:116)
>>>>         at
>>>> org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:445)
>>>>         at
>>>> org.apache.coyote.http11.AbstractHttp11Processor.process(AbstractHttp11Processor.java:1115)
>>>>         at
>>>> org.apache.coyote.AbstractProtocol$AbstractConnectionHandler.process(AbstractProtocol.java:637)
>>>>         at
>>>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.doRun(AprEndpoint.java:2555)
>>>>         at
>>>> org.apache.tomcat.util.net.AprEndpoint$SocketProcessor.run(AprEndpoint.java:2544)
>>>>         at
>>>> java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
>>>>         at
>>>> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
>>>>         at
>>>> org.apache.tomcat.util.threads.TaskThread$WrappingRunnable.run(TaskThread.java:61)
>>>>         at java.lang.Thread.run(Thread.java:748)
>>>>
>>>> 2. According to the error message, I have tested to 1) set
>>>> genomicRegionSearch.enableStrandSpecificSearch = false in
>>>> web.properties file;
>>>>
>>>> 2) I comment the following lines in
>>>> apache-tomcat-7.0.85/webapps/testmine/model/genomicRegionSearchOptionsBase.jsp
>>>> file.
>>>>
>>>>                     <c:if
>>>> test="${WEB_PROPERTIES['genomicRegionSearch.enableStrandSpecificSearch']}">
>>>>                         <li id="genomicRegionStrandSpecific">
>>>>                             <html:checkbox property="strandSpecific"
>>>> value="true" />
>>>>                             <span>Check this box to perform a
>>>> strand-specific region search (search <b>+</b> strand if region
>>>> start&lt;end; search <b>&ndash;</b> strand if region
>>>> end&lt;start)</span>
>>>>                         </li>
>>>>                     </c:if>
>>>>
>>>> However, the error remains.
>>>>
>>>> Could someone help me out?
>>>>
>>>> Best,
>>>>
>>>> Pengcheng Yang
>>>>
>>>> _______________________________________________
>>>> dev mailing list
>>>> [hidden email]
>>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>>
>>>
>>> _______________________________________________
>>> dev mailing list
>>> [hidden email]
>>> https://lists.intermine.org/mailman/listinfo/dev
>>>
>>
>
_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev