blast intermine xml

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

blast intermine xml

Sofia Robb
Hi,

I am trying to write a blast intermine xml. I am getting errors when loading it. Does anyone see what I am doing wrong?

Thank you,
Sofia

my Intermine xml
=============
<items>
<item id="1_0" class="DataSource">
<attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
<reference name="OrganismItem" ref_id="1_0" />
</item>
<item id="1_1" class="DataSource">
<attribute name="name" value="uniprot_sprot.fasta_2015_08"/>
</item>
<item id="2_0" class="DataSet">
<attribute name="name" value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
<collection name="DataSources">
<reference name="DataSourceItem" ref_id="1_0" />
<reference name="DataSourceItem" ref_id="1_1" />
</collection>
</item>
<item id="5_1" class="BlastResult">
<attribute name="queryName" value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
<attribute name="database" value="Uniprot_Swissprot"/>
<attribute name="algorithm" value="blastx"/>
<collection name="DataSources">
<reference name="DataSourceItem" ref_id="1_0" />
<reference name="DataSourceItem" ref_id="1_1" />
</collection>
<reference name="QueryOrganismItem" ref_id="0_0" />
</item>
<item id="6_1" class="BlastHit">
<attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
<attribute name="score" value="7e-12"/>
<attribute name="scoreType" value="BlastHit_evalue"/>
<attribute name="description" value="Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa GN=MGAT2 PE=3 SV=1"/>
<reference name="BlastResultItem" ref_id="5_1" />
</item>
<item id="7_1" class="BlastHSP">
<attribute name="score" value="7e-12"/>
<attribute name="scoreType" value="BlastHSP_evalue"/>
<reference name="BlastHitItem" ref_id="6_1" />
<reference name="HitOrganismItem" ref_id="0_1" />
<reference name="HitBioentityItem" ref_id="3_1" />
<reference name="QueryOrganismItem" ref_id="0_0" />
<reference name="QueryBioentityItem" ref_id="3_2" />
</item>
<item id="4_2" class="Location">
<attribute name="start" value="3"/>
<attribute name="end" value="59"/>
<attribute name="strand" value="+"/>
<reference name="locatedOn" ref_id="3_2" />
</item>
<item id="4_1" class="Location">
<attribute name="start" value="338"/>
<attribute name="end" value="356"/>
<attribute name="strand" value="+"/>
<reference name="locatedOn" ref_id="3_1" />
</item>
<item id="0_0" class="Organism">
<attribute name="genus" value="Schmidtea"/>
<attribute name="species" value="mediterranea "/>
<attribute name="taxonId" value="79327"/>
<attribute name="commonName" value="Freshwater planarian flatworm"/>
</item>
<item id="0_1" class="Organism">
<attribute name="genus" value="Sus"/>
<attribute name="species" value="scrofa "/>
<attribute name="taxonId" value="9823"/>
<attribute name="commonName" value="Pig"/>
</item>
<item id="3_1" class="BioEntity">
<attribute name="name" value="sp|O19071|MGAT2_PIG"/>
<attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
<reference name="organism" ref_id="0_1" />
</item>
<item id="3_2" class="BioEntity">
<attribute name="name" value="mk5-SmedSxl-v31.033737-0.1-1"/>
<attribute name="primaryIdentifier" value="mk5-SmedSxl-v31.033737-0.1-1"/>
<attribute name="secondaryIdentifier" value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
<reference name="organism" ref_id="0_0" />
</item>
</items>

My blast_additions.xml
======================
<classes>
<!-- add any <class> elements here -->
  <class name="BlastResult" is-interface="true" >
    <attribute name="queryName" type="java.lang.String"/>
    <attribute name="database" type="java.lang.String"/>
    <attribute name="algorithm" type="java.lang.String"/>
    <collection name="DataSources" referenced-type="DataSource" />
    <reference name="QueryOrganismItem" referenced-type="Organism" />
  </class>
  <class name="BlastHit" extends="Gene" is-interface="true">
    <reference name="blastResult" referenced-type="BlastResult" />
  </class>
  <class name="BlastHSP" extends="SequenceFeature" is-interface="true">
    <reference name="blastHit" referenced-type="BlastHit"/>
  </class>
</classes>


My Error
=======

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:201: Exception while reading from: /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
at org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
at org.intermine.task.Integrate.performAction(Integrate.java:223)
at org.intermine.task.Integrate.performAction(Integrate.java:135)
at org.intermine.task.Integrate.execute(Integrate.java:127)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.Main.runBuild(Main.java:851)
at org.apache.tools.ant.Main.startAnt(Main.java:235)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: org.intermine.InterMineException: Error during unmarshalling
at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
at org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
at org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
... 31 more
Caused by: java.lang.NullPointerException
at java.lang.Class.isAssignableFrom(Native Method)
at org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
... 33 more

Total time: 14 seconds

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Julie Sullivan
Hi Sofia!

Sorry you are having problems.

1. The additions file you give doesn't have the whole model. e.g.
BlastHSP has fields in your items XML that aren't listed in your additions.

Maybe because they are somewhere else in your model?

2. The XML is formatted incorrectly, e.g. here:

        <collection name="DataSources">
                <reference name="DataSourceItem" ref_id="1_0" />
                <reference name="DataSourceItem" ref_id="1_1" />
        </collection>

Should be something like:

        <collection name="DataSources">
                <reference ref_id="1_0" />
                <reference ref_id="1_1" />
        </collection>

Although I don't know if that's what's causing your problems.

3. I am guessing you are making the XML by hand. I do know some people
who do this but most people use the Java or Perl API. It makes life
easier! :)

http://intermine.readthedocs.org/en/latest/database/data-sources/apis/

Make the above fix and try again (be sure to use the -v tag in your
command too if you aren't already), and let me know if that doesn't work.

Julie

On 29/10/15 19:37, Sofia Robb wrote:

> Hi,
>
> I am trying to write a blast intermine xml. I am getting errors when
> loading it. Does anyone see what I am doing wrong?
>
> Thank you,
> Sofia
>
> my Intermine xml
> =============
> <items>
> <item id="1_0" class="DataSource">
> <attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
> <reference name="OrganismItem" ref_id="1_0" />
> </item>
> <item id="1_1" class="DataSource">
> <attribute name="name" value="uniprot_sprot.fasta_2015_08"/>
> </item>
> <item id="2_0" class="DataSet">
> <attribute name="name" value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
> <collection name="DataSources">
> <reference name="DataSourceItem" ref_id="1_0" />
> <reference name="DataSourceItem" ref_id="1_1" />
> </collection>
> </item>
> <item id="5_1" class="BlastResult">
> <attribute name="queryName"
> value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
> <attribute name="database" value="Uniprot_Swissprot"/>
> <attribute name="algorithm" value="blastx"/>
> <collection name="DataSources">
> <reference name="DataSourceItem" ref_id="1_0" />
> <reference name="DataSourceItem" ref_id="1_1" />
> </collection>
> <reference name="QueryOrganismItem" ref_id="0_0" />
> </item>
> <item id="6_1" class="BlastHit">
> <attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
> <attribute name="score" value="7e-12"/>
> <attribute name="scoreType" value="BlastHit_evalue"/>
> <attribute name="description" value="Alpha-1,6-mannosyl-glycoprotein
> 2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa GN=MGAT2 PE=3 SV=1"/>
> <reference name="BlastResultItem" ref_id="5_1" />
> </item>
> <item id="7_1" class="BlastHSP">
> <attribute name="score" value="7e-12"/>
> <attribute name="scoreType" value="BlastHSP_evalue"/>
> <reference name="BlastHitItem" ref_id="6_1" />
> <reference name="HitOrganismItem" ref_id="0_1" />
> <reference name="HitBioentityItem" ref_id="3_1" />
> <reference name="QueryOrganismItem" ref_id="0_0" />
> <reference name="QueryBioentityItem" ref_id="3_2" />
> </item>
> <item id="4_2" class="Location">
> <attribute name="start" value="3"/>
> <attribute name="end" value="59"/>
> <attribute name="strand" value="+"/>
> <reference name="locatedOn" ref_id="3_2" />
> </item>
> <item id="4_1" class="Location">
> <attribute name="start" value="338"/>
> <attribute name="end" value="356"/>
> <attribute name="strand" value="+"/>
> <reference name="locatedOn" ref_id="3_1" />
> </item>
> <item id="0_0" class="Organism">
> <attribute name="genus" value="Schmidtea"/>
> <attribute name="species" value="mediterranea "/>
> <attribute name="taxonId" value="79327"/>
> <attribute name="commonName" value="Freshwater planarian flatworm"/>
> </item>
> <item id="0_1" class="Organism">
> <attribute name="genus" value="Sus"/>
> <attribute name="species" value="scrofa "/>
> <attribute name="taxonId" value="9823"/>
> <attribute name="commonName" value="Pig"/>
> </item>
> <item id="3_1" class="BioEntity">
> <attribute name="name" value="sp|O19071|MGAT2_PIG"/>
> <attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
> <reference name="organism" ref_id="0_1" />
> </item>
> <item id="3_2" class="BioEntity">
> <attribute name="name" value="mk5-SmedSxl-v31.033737-0.1-1"/>
> <attribute name="primaryIdentifier" value="mk5-SmedSxl-v31.033737-0.1-1"/>
> <attribute name="secondaryIdentifier"
> value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
> <reference name="organism" ref_id="0_0" />
> </item>
> </items>
>
> My blast_additions.xml
> ======================
> <classes>
> <!-- add any <class> elements here -->
>    <class name="BlastResult" is-interface="true" >
>      <attribute name="queryName" type="java.lang.String"/>
>      <attribute name="database" type="java.lang.String"/>
>      <attribute name="algorithm" type="java.lang.String"/>
>      <collection name="DataSources" referenced-type="DataSource" />
>      <reference name="QueryOrganismItem" referenced-type="Organism" />
>    </class>
>    <class name="BlastHit" extends="Gene" is-interface="true">
>      <reference name="blastResult" referenced-type="BlastResult" />
>    </class>
>    <class name="BlastHSP" extends="SequenceFeature" is-interface="true">
>      <reference name="blastHit" referenced-type="BlastHit"/>
>    </class>
> </classes>
>
>
> My Error
> =======
>
> BUILD FAILED
> /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
> following error occurred while executing this line:
> /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201: Exception
> while reading from:
> /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
> at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:435)
> at org.apache.tools.ant.Target.performTasks(Target.java:456)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
> at
> org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
> at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
> at org.intermine.task.Integrate.performAction(Integrate.java:223)
> at org.intermine.task.Integrate.performAction(Integrate.java:135)
> at org.intermine.task.Integrate.execute(Integrate.java:127)
> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
> at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
> at
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> at java.lang.reflect.Method.invoke(Method.java:606)
> at
> org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
> at org.apache.tools.ant.Task.perform(Task.java:348)
> at org.apache.tools.ant.Target.execute(Target.java:435)
> at org.apache.tools.ant.Target.performTasks(Target.java:456)
> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
> at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
> at
> org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
> at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
> at org.apache.tools.ant.Main.runBuild(Main.java:851)
> at org.apache.tools.ant.Main.startAnt(Main.java:235)
> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
> Caused by: org.intermine.InterMineException: Error during unmarshalling
> at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
> at org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
> at
> org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
> ... 31 more
> Caused by: java.lang.NullPointerException
> at java.lang.Class.isAssignableFrom(Native Method)
> at org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
> at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
> at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
> at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
> ... 33 more
>
> Total time: 14 seconds
>
>
> _______________________________________________
> dev mailing list
> [hidden email]
> http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Sofia Robb
Hi Julie,

If you mean my own perl script when you say by hand, then yes.  I thought that if I use the extend ' <class name="BlastHSP" extends="SequenceFeature" is-interface="true">' that I could use whatever fields that this class can use.  Is this not true? I removed the name field in the reference items in all collections. This still did not help. I will explore the perl API.

Thank you,
Sofia

On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan <[hidden email]> wrote:
Hi Sofia!

Sorry you are having problems.

1. The additions file you give doesn't have the whole model. e.g. BlastHSP has fields in your items XML that aren't listed in your additions.

Maybe because they are somewhere else in your model?

2. The XML is formatted incorrectly, e.g. here:

        <collection name="DataSources">
                <reference name="DataSourceItem" ref_id="1_0" />
                <reference name="DataSourceItem" ref_id="1_1" />
        </collection>

Should be something like:

        <collection name="DataSources">
                <reference ref_id="1_0" />
                <reference ref_id="1_1" />
        </collection>

Although I don't know if that's what's causing your problems.

3. I am guessing you are making the XML by hand. I do know some people who do this but most people use the Java or Perl API. It makes life easier! :)

http://intermine.readthedocs.org/en/latest/database/data-sources/apis/

Make the above fix and try again (be sure to use the -v tag in your command too if you aren't already), and let me know if that doesn't work.

Julie


On 29/10/15 19:37, Sofia Robb wrote:
Hi,

I am trying to write a blast intermine xml. I am getting errors when
loading it. Does anyone see what I am doing wrong?

Thank you,
Sofia

my Intermine xml
=============
<items>
<item id="1_0" class="DataSource">
<attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
<reference name="OrganismItem" ref_id="1_0" />
</item>
<item id="1_1" class="DataSource">
<attribute name="name" value="uniprot_sprot.fasta_2015_08"/>
</item>
<item id="2_0" class="DataSet">
<attribute name="name" value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
<collection name="DataSources">
<reference name="DataSourceItem" ref_id="1_0" />
<reference name="DataSourceItem" ref_id="1_1" />
</collection>
</item>
<item id="5_1" class="BlastResult">
<attribute name="queryName"
value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
<attribute name="database" value="Uniprot_Swissprot"/>
<attribute name="algorithm" value="blastx"/>
<collection name="DataSources">
<reference name="DataSourceItem" ref_id="1_0" />
<reference name="DataSourceItem" ref_id="1_1" />
</collection>
<reference name="QueryOrganismItem" ref_id="0_0" />
</item>
<item id="6_1" class="BlastHit">
<attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
<attribute name="score" value="7e-12"/>
<attribute name="scoreType" value="BlastHit_evalue"/>
<attribute name="description" value="Alpha-1,6-mannosyl-glycoprotein
2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa GN=MGAT2 PE=3 SV=1"/>
<reference name="BlastResultItem" ref_id="5_1" />
</item>
<item id="7_1" class="BlastHSP">
<attribute name="score" value="7e-12"/>
<attribute name="scoreType" value="BlastHSP_evalue"/>
<reference name="BlastHitItem" ref_id="6_1" />
<reference name="HitOrganismItem" ref_id="0_1" />
<reference name="HitBioentityItem" ref_id="3_1" />
<reference name="QueryOrganismItem" ref_id="0_0" />
<reference name="QueryBioentityItem" ref_id="3_2" />
</item>
<item id="4_2" class="Location">
<attribute name="start" value="3"/>
<attribute name="end" value="59"/>
<attribute name="strand" value="+"/>
<reference name="locatedOn" ref_id="3_2" />
</item>
<item id="4_1" class="Location">
<attribute name="start" value="338"/>
<attribute name="end" value="356"/>
<attribute name="strand" value="+"/>
<reference name="locatedOn" ref_id="3_1" />
</item>
<item id="0_0" class="Organism">
<attribute name="genus" value="Schmidtea"/>
<attribute name="species" value="mediterranea "/>
<attribute name="taxonId" value="79327"/>
<attribute name="commonName" value="Freshwater planarian flatworm"/>
</item>
<item id="0_1" class="Organism">
<attribute name="genus" value="Sus"/>
<attribute name="species" value="scrofa "/>
<attribute name="taxonId" value="9823"/>
<attribute name="commonName" value="Pig"/>
</item>
<item id="3_1" class="BioEntity">
<attribute name="name" value="sp|O19071|MGAT2_PIG"/>
<attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
<reference name="organism" ref_id="0_1" />
</item>
<item id="3_2" class="BioEntity">
<attribute name="name" value="mk5-SmedSxl-v31.033737-0.1-1"/>
<attribute name="primaryIdentifier" value="mk5-SmedSxl-v31.033737-0.1-1"/>
<attribute name="secondaryIdentifier"
value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
<reference name="organism" ref_id="0_0" />
</item>
</items>

My blast_additions.xml
======================
<classes>
<!-- add any <class> elements here -->
   <class name="BlastResult" is-interface="true" >
     <attribute name="queryName" type="java.lang.String"/>
     <attribute name="database" type="java.lang.String"/>
     <attribute name="algorithm" type="java.lang.String"/>
     <collection name="DataSources" referenced-type="DataSource" />
     <reference name="QueryOrganismItem" referenced-type="Organism" />
   </class>
   <class name="BlastHit" extends="Gene" is-interface="true">
     <reference name="blastResult" referenced-type="BlastResult" />
   </class>
   <class name="BlastHSP" extends="SequenceFeature" is-interface="true">
     <reference name="blastHit" referenced-type="BlastHit"/>
   </class>
</classes>


My Error
=======

BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:201: Exception
while reading from:
/data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
at
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at
org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
at org.intermine.task.Integrate.performAction(Integrate.java:223)
at org.intermine.task.Integrate.performAction(Integrate.java:135)
at org.intermine.task.Integrate.execute(Integrate.java:127)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at
org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
at
org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.Main.runBuild(Main.java:851)
at org.apache.tools.ant.Main.startAnt(Main.java:235)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: org.intermine.InterMineException: Error during unmarshalling
at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
at org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
at
org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
... 31 more
Caused by: java.lang.NullPointerException
at java.lang.Class.isAssignableFrom(Native Method)
at org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
at org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
... 33 more

Total time: 14 seconds


_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev



_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Julie Sullivan
Hi Sofia,

1. The Perl API will do a lot of things for you, like create the XML.

2. Yes, you are right. Extending SequenceFeature will cause your object,
BlastHSP, to inherit all it's references and collections.

Specifically I was referring to these references in BlastHSP that are in
the items XML:

 >         <reference name="BlastHitItem" ref_id="6_1" />
 >         <reference name="HitOrganismItem" ref_id="0_1" />
 >         <reference name="HitBioentityItem" ref_id="3_1" />
 >         <reference name="QueryOrganismItem" ref_id="0_0" />
 >         <reference name="QueryBioentityItem" ref_id="3_2" />

They are not in your additions.xml.


On 30/10/15 15:03, Sofia Robb wrote:

> Hi Julie,
>
> If you mean my own perl script when you say by hand, then yes. I thought
> that if I use the extend '<class name="BlastHSP"
> extends="SequenceFeature" is-interface="true">' that I could use
> whatever fields that this class can use.  Is this not true? I removed
> the name field in the reference items in all collections. This still did
> not help. I will explore the perl API.
>
> Thank you,
> Sofia
>
> On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Sofia!
>
>     Sorry you are having problems.
>
>     1. The additions file you give doesn't have the whole model. e.g.
>     BlastHSP has fields in your items XML that aren't listed in your
>     additions.
>
>     Maybe because they are somewhere else in your model?
>
>     2. The XML is formatted incorrectly, e.g. here:
>
>              <collection name="DataSources">
>                      <reference name="DataSourceItem" ref_id="1_0" />
>                      <reference name="DataSourceItem" ref_id="1_1" />
>              </collection>
>
>     Should be something like:
>
>              <collection name="DataSources">
>                      <reference ref_id="1_0" />
>                      <reference ref_id="1_1" />
>              </collection>
>
>     Although I don't know if that's what's causing your problems.
>
>     3. I am guessing you are making the XML by hand. I do know some
>     people who do this but most people use the Java or Perl API. It
>     makes life easier! :)
>
>     http://intermine.readthedocs.org/en/latest/database/data-sources/apis/
>
>     Make the above fix and try again (be sure to use the -v tag in your
>     command too if you aren't already), and let me know if that doesn't
>     work.
>
>     Julie
>
>
>     On 29/10/15 19:37, Sofia Robb wrote:
>
>         Hi,
>
>         I am trying to write a blast intermine xml. I am getting errors when
>         loading it. Does anyone see what I am doing wrong?
>
>         Thank you,
>         Sofia
>
>         my Intermine xml
>         =============
>         <items>
>         <item id="1_0" class="DataSource">
>         <attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
>         <reference name="OrganismItem" ref_id="1_0" />
>         </item>
>         <item id="1_1" class="DataSource">
>         <attribute name="name" value="uniprot_sprot.fasta_2015_08"/>
>         </item>
>         <item id="2_0" class="DataSet">
>         <attribute name="name"
>         value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
>         <collection name="DataSources">
>         <reference name="DataSourceItem" ref_id="1_0" />
>         <reference name="DataSourceItem" ref_id="1_1" />
>         </collection>
>         </item>
>         <item id="5_1" class="BlastResult">
>         <attribute name="queryName"
>         value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
>         <attribute name="database" value="Uniprot_Swissprot"/>
>         <attribute name="algorithm" value="blastx"/>
>         <collection name="DataSources">
>         <reference name="DataSourceItem" ref_id="1_0" />
>         <reference name="DataSourceItem" ref_id="1_1" />
>         </collection>
>         <reference name="QueryOrganismItem" ref_id="0_0" />
>         </item>
>         <item id="6_1" class="BlastHit">
>         <attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
>         <attribute name="score" value="7e-12"/>
>         <attribute name="scoreType" value="BlastHit_evalue"/>
>         <attribute name="description" value="Alpha-1,6-mannosyl-glycoprotein
>         2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa GN=MGAT2
>         PE=3 SV=1"/>
>         <reference name="BlastResultItem" ref_id="5_1" />
>         </item>
>         <item id="7_1" class="BlastHSP">
>         <attribute name="score" value="7e-12"/>
>         <attribute name="scoreType" value="BlastHSP_evalue"/>
>         <reference name="BlastHitItem" ref_id="6_1" />
>         <reference name="HitOrganismItem" ref_id="0_1" />
>         <reference name="HitBioentityItem" ref_id="3_1" />
>         <reference name="QueryOrganismItem" ref_id="0_0" />
>         <reference name="QueryBioentityItem" ref_id="3_2" />
>         </item>
>         <item id="4_2" class="Location">
>         <attribute name="start" value="3"/>
>         <attribute name="end" value="59"/>
>         <attribute name="strand" value="+"/>
>         <reference name="locatedOn" ref_id="3_2" />
>         </item>
>         <item id="4_1" class="Location">
>         <attribute name="start" value="338"/>
>         <attribute name="end" value="356"/>
>         <attribute name="strand" value="+"/>
>         <reference name="locatedOn" ref_id="3_1" />
>         </item>
>         <item id="0_0" class="Organism">
>         <attribute name="genus" value="Schmidtea"/>
>         <attribute name="species" value="mediterranea "/>
>         <attribute name="taxonId" value="79327"/>
>         <attribute name="commonName" value="Freshwater planarian flatworm"/>
>         </item>
>         <item id="0_1" class="Organism">
>         <attribute name="genus" value="Sus"/>
>         <attribute name="species" value="scrofa "/>
>         <attribute name="taxonId" value="9823"/>
>         <attribute name="commonName" value="Pig"/>
>         </item>
>         <item id="3_1" class="BioEntity">
>         <attribute name="name" value="sp|O19071|MGAT2_PIG"/>
>         <attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
>         <reference name="organism" ref_id="0_1" />
>         </item>
>         <item id="3_2" class="BioEntity">
>         <attribute name="name" value="mk5-SmedSxl-v31.033737-0.1-1"/>
>         <attribute name="primaryIdentifier"
>         value="mk5-SmedSxl-v31.033737-0.1-1"/>
>         <attribute name="secondaryIdentifier"
>         value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
>         <reference name="organism" ref_id="0_0" />
>         </item>
>         </items>
>
>         My blast_additions.xml
>         ======================
>         <classes>
>         <!-- add any <class> elements here -->
>             <class name="BlastResult" is-interface="true" >
>               <attribute name="queryName" type="java.lang.String"/>
>               <attribute name="database" type="java.lang.String"/>
>               <attribute name="algorithm" type="java.lang.String"/>
>               <collection name="DataSources" referenced-type="DataSource" />
>               <reference name="QueryOrganismItem"
>         referenced-type="Organism" />
>             </class>
>             <class name="BlastHit" extends="Gene" is-interface="true">
>               <reference name="blastResult" referenced-type="BlastResult" />
>             </class>
>             <class name="BlastHSP" extends="SequenceFeature"
>         is-interface="true">
>               <reference name="blastHit" referenced-type="BlastHit"/>
>             </class>
>         </classes>
>
>
>         My Error
>         =======
>
>         BUILD FAILED
>         /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
>         following error occurred while executing this line:
>         /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201:
>         Exception
>         while reading from:
>         /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
>         at
>         org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
>         at
>         org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
>         sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:606)
>         at
>         org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>         at org.apache.tools.ant.Target.execute(Target.java:435)
>         at org.apache.tools.ant.Target.performTasks(Target.java:456)
>         at
>         org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>         at
>         org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>         at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>         at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
>         at org.intermine.task.Integrate.performAction(Integrate.java:223)
>         at org.intermine.task.Integrate.performAction(Integrate.java:135)
>         at org.intermine.task.Integrate.execute(Integrate.java:127)
>         at
>         org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>         at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
>         at
>         sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>         at java.lang.reflect.Method.invoke(Method.java:606)
>         at
>         org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>         at org.apache.tools.ant.Task.perform(Task.java:348)
>         at org.apache.tools.ant.Target.execute(Target.java:435)
>         at org.apache.tools.ant.Target.performTasks(Target.java:456)
>         at
>         org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>         at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
>         at
>         org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>         at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>         at org.apache.tools.ant.Main.runBuild(Main.java:851)
>         at org.apache.tools.ant.Main.startAnt(Main.java:235)
>         at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>         at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>         Caused by: org.intermine.InterMineException: Error during
>         unmarshalling
>         at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
>         at
>         org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
>         at
>         org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
>         ... 31 more
>         Caused by: java.lang.NullPointerException
>         at java.lang.Class.isAssignableFrom(Native Method)
>         at
>         org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
>         at
>         org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
>         at
>         org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
>         at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
>         ... 33 more
>
>         Total time: 14 seconds
>
>
>         _______________________________________________
>         dev mailing list
>         [hidden email] <mailto:[hidden email]>
>         http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Sofia Robb
Do the reference items need to have the same name field as in the model? I that that as long as the type was the same, it was ok. Also, if I want to have two organism references, both have to be in my model?

Thank you for your help,
Sofia

On Fri, Oct 30, 2015 at 11:07 AM, Julie Sullivan <[hidden email]> wrote:
Hi Sofia,

1. The Perl API will do a lot of things for you, like create the XML.

2. Yes, you are right. Extending SequenceFeature will cause your object, BlastHSP, to inherit all it's references and collections.

Specifically I was referring to these references in BlastHSP that are in the items XML:

>         <reference name="BlastHitItem" ref_id="6_1" />
>         <reference name="HitOrganismItem" ref_id="0_1" />
>         <reference name="HitBioentityItem" ref_id="3_1" />
>         <reference name="QueryOrganismItem" ref_id="0_0" />
>         <reference name="QueryBioentityItem" ref_id="3_2" />

They are not in your additions.xml.


On 30/10/15 15:03, Sofia Robb wrote:
Hi Julie,

If you mean my own perl script when you say by hand, then yes. I thought
that if I use the extend '<class name="BlastHSP"
extends="SequenceFeature" is-interface="true">' that I could use
whatever fields that this class can use.  Is this not true? I removed
the name field in the reference items in all collections. This still did
not help. I will explore the perl API.

Thank you,
Sofia

On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi Sofia!

    Sorry you are having problems.

    1. The additions file you give doesn't have the whole model. e.g.
    BlastHSP has fields in your items XML that aren't listed in your
    additions.

    Maybe because they are somewhere else in your model?

    2. The XML is formatted incorrectly, e.g. here:

             <collection name="DataSources">
                     <reference name="DataSourceItem" ref_id="1_0" />
                     <reference name="DataSourceItem" ref_id="1_1" />
             </collection>

    Should be something like:

             <collection name="DataSources">
                     <reference ref_id="1_0" />
                     <reference ref_id="1_1" />
             </collection>

    Although I don't know if that's what's causing your problems.

    3. I am guessing you are making the XML by hand. I do know some
    people who do this but most people use the Java or Perl API. It
    makes life easier! :)

    http://intermine.readthedocs.org/en/latest/database/data-sources/apis/

    Make the above fix and try again (be sure to use the -v tag in your
    command too if you aren't already), and let me know if that doesn't
    work.

    Julie


    On 29/10/15 19:37, Sofia Robb wrote:

        Hi,

        I am trying to write a blast intermine xml. I am getting errors when
        loading it. Does anyone see what I am doing wrong?

        Thank you,
        Sofia

        my Intermine xml
        =============
        <items>
        <item id="1_0" class="DataSource">
        <attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
        <reference name="OrganismItem" ref_id="1_0" />
        </item>
        <item id="1_1" class="DataSource">
        <attribute name="name" value="uniprot_sprot.fasta_2015_08"/>
        </item>
        <item id="2_0" class="DataSet">
        <attribute name="name"
        value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
        <collection name="DataSources">
        <reference name="DataSourceItem" ref_id="1_0" />
        <reference name="DataSourceItem" ref_id="1_1" />
        </collection>
        </item>
        <item id="5_1" class="BlastResult">
        <attribute name="queryName"
        value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
        <attribute name="database" value="Uniprot_Swissprot"/>
        <attribute name="algorithm" value="blastx"/>
        <collection name="DataSources">
        <reference name="DataSourceItem" ref_id="1_0" />
        <reference name="DataSourceItem" ref_id="1_1" />
        </collection>
        <reference name="QueryOrganismItem" ref_id="0_0" />
        </item>
        <item id="6_1" class="BlastHit">
        <attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
        <attribute name="score" value="7e-12"/>
        <attribute name="scoreType" value="BlastHit_evalue"/>
        <attribute name="description" value="Alpha-1,6-mannosyl-glycoprotein
        2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa GN=MGAT2
        PE=3 SV=1"/>
        <reference name="BlastResultItem" ref_id="5_1" />
        </item>
        <item id="7_1" class="BlastHSP">
        <attribute name="score" value="7e-12"/>
        <attribute name="scoreType" value="BlastHSP_evalue"/>
        <reference name="BlastHitItem" ref_id="6_1" />
        <reference name="HitOrganismItem" ref_id="0_1" />
        <reference name="HitBioentityItem" ref_id="3_1" />
        <reference name="QueryOrganismItem" ref_id="0_0" />
        <reference name="QueryBioentityItem" ref_id="3_2" />
        </item>
        <item id="4_2" class="Location">
        <attribute name="start" value="3"/>
        <attribute name="end" value="59"/>
        <attribute name="strand" value="+"/>
        <reference name="locatedOn" ref_id="3_2" />
        </item>
        <item id="4_1" class="Location">
        <attribute name="start" value="338"/>
        <attribute name="end" value="356"/>
        <attribute name="strand" value="+"/>
        <reference name="locatedOn" ref_id="3_1" />
        </item>
        <item id="0_0" class="Organism">
        <attribute name="genus" value="Schmidtea"/>
        <attribute name="species" value="mediterranea "/>
        <attribute name="taxonId" value="79327"/>
        <attribute name="commonName" value="Freshwater planarian flatworm"/>
        </item>
        <item id="0_1" class="Organism">
        <attribute name="genus" value="Sus"/>
        <attribute name="species" value="scrofa "/>
        <attribute name="taxonId" value="9823"/>
        <attribute name="commonName" value="Pig"/>
        </item>
        <item id="3_1" class="BioEntity">
        <attribute name="name" value="sp|O19071|MGAT2_PIG"/>
        <attribute name="primaryIdentifier" value="sp|O19071|MGAT2_PIG"/>
        <reference name="organism" ref_id="0_1" />
        </item>
        <item id="3_2" class="BioEntity">
        <attribute name="name" value="mk5-SmedSxl-v31.033737-0.1-1"/>
        <attribute name="primaryIdentifier"
        value="mk5-SmedSxl-v31.033737-0.1-1"/>
        <attribute name="secondaryIdentifier"
        value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
        <reference name="organism" ref_id="0_0" />
        </item>
        </items>

        My blast_additions.xml
        ======================
        <classes>
        <!-- add any <class> elements here -->
            <class name="BlastResult" is-interface="true" >
              <attribute name="queryName" type="java.lang.String"/>
              <attribute name="database" type="java.lang.String"/>
              <attribute name="algorithm" type="java.lang.String"/>
              <collection name="DataSources" referenced-type="DataSource" />
              <reference name="QueryOrganismItem"
        referenced-type="Organism" />
            </class>
            <class name="BlastHit" extends="Gene" is-interface="true">
              <reference name="blastResult" referenced-type="BlastResult" />
            </class>
            <class name="BlastHSP" extends="SequenceFeature"
        is-interface="true">
              <reference name="blastHit" referenced-type="BlastHit"/>
            </class>
        </classes>


        My Error
        =======

        BUILD FAILED
        /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
        following error occurred while executing this line:
        /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201:
        Exception
        while reading from:
        /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
        at
        org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
        at
        org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
        sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at
        org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:435)
        at org.apache.tools.ant.Target.performTasks(Target.java:456)
        at
        org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
        at
        org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
        at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
        at org.intermine.task.Integrate.performAction(Integrate.java:223)
        at org.intermine.task.Integrate.performAction(Integrate.java:135)
        at org.intermine.task.Integrate.execute(Integrate.java:127)
        at
        org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
        at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
        at
        sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:606)
        at
        org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
        at org.apache.tools.ant.Task.perform(Task.java:348)
        at org.apache.tools.ant.Target.execute(Target.java:435)
        at org.apache.tools.ant.Target.performTasks(Target.java:456)
        at
        org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
        at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
        at
        org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
        at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
        at org.apache.tools.ant.Main.runBuild(Main.java:851)
        at org.apache.tools.ant.Main.startAnt(Main.java:235)
        at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
        at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
        Caused by: org.intermine.InterMineException: Error during
        unmarshalling
        at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
        at
        org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
        at
        org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
        ... 31 more
        Caused by: java.lang.NullPointerException
        at java.lang.Class.isAssignableFrom(Native Method)
        at
        org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
        at
        org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
        at
        org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
        at org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
        ... 33 more

        Total time: 14 seconds


        _______________________________________________
        dev mailing list
        [hidden email] <mailto:[hidden email]>
        http://mail.intermine.org/cgi-bin/mailman/listinfo/dev




_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Julie Sullivan


On 30/10/15 15:15, Sofia Robb wrote:
> Do the reference items need to have the same name field as in the model?

Yes. The object you are storing has to match an object in the data model.

> I that that as long as the type was the same, it was ok. Also, if I want
> to have two organism references, both have to be in my model?

Yes. Everything you want to put in the database has to be in your model.

If your script is on github or somewhere public, I can try to help. :)

Julie

> Thank you for your help,
> Sofia
>
> On Fri, Oct 30, 2015 at 11:07 AM, Julie Sullivan <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Sofia,
>
>     1. The Perl API will do a lot of things for you, like create the XML.
>
>     2. Yes, you are right. Extending SequenceFeature will cause your
>     object, BlastHSP, to inherit all it's references and collections.
>
>     Specifically I was referring to these references in BlastHSP that
>     are in the items XML:
>
>     >         <reference name="BlastHitItem" ref_id="6_1" />
>     >         <reference name="HitOrganismItem" ref_id="0_1" />
>     >         <reference name="HitBioentityItem" ref_id="3_1" />
>     >         <reference name="QueryOrganismItem" ref_id="0_0" />
>     >         <reference name="QueryBioentityItem" ref_id="3_2" />
>
>     They are not in your additions.xml.
>
>
>     On 30/10/15 15:03, Sofia Robb wrote:
>
>         Hi Julie,
>
>         If you mean my own perl script when you say by hand, then yes. I
>         thought
>         that if I use the extend '<class name="BlastHSP"
>         extends="SequenceFeature" is-interface="true">' that I could use
>         whatever fields that this class can use.  Is this not true? I
>         removed
>         the name field in the reference items in all collections. This
>         still did
>         not help. I will explore the perl API.
>
>         Thank you,
>         Sofia
>
>         On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan
>         <[hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>              Hi Sofia!
>
>              Sorry you are having problems.
>
>              1. The additions file you give doesn't have the whole
>         model. e.g.
>              BlastHSP has fields in your items XML that aren't listed in
>         your
>              additions.
>
>              Maybe because they are somewhere else in your model?
>
>              2. The XML is formatted incorrectly, e.g. here:
>
>                       <collection name="DataSources">
>                               <reference name="DataSourceItem"
>         ref_id="1_0" />
>                               <reference name="DataSourceItem"
>         ref_id="1_1" />
>                       </collection>
>
>              Should be something like:
>
>                       <collection name="DataSources">
>                               <reference ref_id="1_0" />
>                               <reference ref_id="1_1" />
>                       </collection>
>
>              Although I don't know if that's what's causing your problems.
>
>              3. I am guessing you are making the XML by hand. I do know some
>              people who do this but most people use the Java or Perl API. It
>              makes life easier! :)
>
>         http://intermine.readthedocs.org/en/latest/database/data-sources/apis/
>
>              Make the above fix and try again (be sure to use the -v tag
>         in your
>              command too if you aren't already), and let me know if that
>         doesn't
>              work.
>
>              Julie
>
>
>              On 29/10/15 19:37, Sofia Robb wrote:
>
>                  Hi,
>
>                  I am trying to write a blast intermine xml. I am
>         getting errors when
>                  loading it. Does anyone see what I am doing wrong?
>
>                  Thank you,
>                  Sofia
>
>                  my Intermine xml
>                  =============
>                  <items>
>                  <item id="1_0" class="DataSource">
>                  <attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
>                  <reference name="OrganismItem" ref_id="1_0" />
>                  </item>
>                  <item id="1_1" class="DataSource">
>                  <attribute name="name"
>         value="uniprot_sprot.fasta_2015_08"/>
>                  </item>
>                  <item id="2_0" class="DataSet">
>                  <attribute name="name"
>                  value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
>                  <collection name="DataSources">
>                  <reference name="DataSourceItem" ref_id="1_0" />
>                  <reference name="DataSourceItem" ref_id="1_1" />
>                  </collection>
>                  </item>
>                  <item id="5_1" class="BlastResult">
>                  <attribute name="queryName"
>
>         value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
>                  <attribute name="database" value="Uniprot_Swissprot"/>
>                  <attribute name="algorithm" value="blastx"/>
>                  <collection name="DataSources">
>                  <reference name="DataSourceItem" ref_id="1_0" />
>                  <reference name="DataSourceItem" ref_id="1_1" />
>                  </collection>
>                  <reference name="QueryOrganismItem" ref_id="0_0" />
>                  </item>
>                  <item id="6_1" class="BlastHit">
>                  <attribute name="primaryIdentifier"
>         value="sp|O19071|MGAT2_PIG"/>
>                  <attribute name="score" value="7e-12"/>
>                  <attribute name="scoreType" value="BlastHit_evalue"/>
>                  <attribute name="description"
>         value="Alpha-1,6-mannosyl-glycoprotein
>                  2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa
>         GN=MGAT2
>                  PE=3 SV=1"/>
>                  <reference name="BlastResultItem" ref_id="5_1" />
>                  </item>
>                  <item id="7_1" class="BlastHSP">
>                  <attribute name="score" value="7e-12"/>
>                  <attribute name="scoreType" value="BlastHSP_evalue"/>
>                  <reference name="BlastHitItem" ref_id="6_1" />
>                  <reference name="HitOrganismItem" ref_id="0_1" />
>                  <reference name="HitBioentityItem" ref_id="3_1" />
>                  <reference name="QueryOrganismItem" ref_id="0_0" />
>                  <reference name="QueryBioentityItem" ref_id="3_2" />
>                  </item>
>                  <item id="4_2" class="Location">
>                  <attribute name="start" value="3"/>
>                  <attribute name="end" value="59"/>
>                  <attribute name="strand" value="+"/>
>                  <reference name="locatedOn" ref_id="3_2" />
>                  </item>
>                  <item id="4_1" class="Location">
>                  <attribute name="start" value="338"/>
>                  <attribute name="end" value="356"/>
>                  <attribute name="strand" value="+"/>
>                  <reference name="locatedOn" ref_id="3_1" />
>                  </item>
>                  <item id="0_0" class="Organism">
>                  <attribute name="genus" value="Schmidtea"/>
>                  <attribute name="species" value="mediterranea "/>
>                  <attribute name="taxonId" value="79327"/>
>                  <attribute name="commonName" value="Freshwater
>         planarian flatworm"/>
>                  </item>
>                  <item id="0_1" class="Organism">
>                  <attribute name="genus" value="Sus"/>
>                  <attribute name="species" value="scrofa "/>
>                  <attribute name="taxonId" value="9823"/>
>                  <attribute name="commonName" value="Pig"/>
>                  </item>
>                  <item id="3_1" class="BioEntity">
>                  <attribute name="name" value="sp|O19071|MGAT2_PIG"/>
>                  <attribute name="primaryIdentifier"
>         value="sp|O19071|MGAT2_PIG"/>
>                  <reference name="organism" ref_id="0_1" />
>                  </item>
>                  <item id="3_2" class="BioEntity">
>                  <attribute name="name"
>         value="mk5-SmedSxl-v31.033737-0.1-1"/>
>                  <attribute name="primaryIdentifier"
>                  value="mk5-SmedSxl-v31.033737-0.1-1"/>
>                  <attribute name="secondaryIdentifier"
>                  value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
>                  <reference name="organism" ref_id="0_0" />
>                  </item>
>                  </items>
>
>                  My blast_additions.xml
>                  ======================
>                  <classes>
>                  <!-- add any <class> elements here -->
>                      <class name="BlastResult" is-interface="true" >
>                        <attribute name="queryName" type="java.lang.String"/>
>                        <attribute name="database" type="java.lang.String"/>
>                        <attribute name="algorithm" type="java.lang.String"/>
>                        <collection name="DataSources"
>         referenced-type="DataSource" />
>                        <reference name="QueryOrganismItem"
>                  referenced-type="Organism" />
>                      </class>
>                      <class name="BlastHit" extends="Gene"
>         is-interface="true">
>                        <reference name="blastResult"
>         referenced-type="BlastResult" />
>                      </class>
>                      <class name="BlastHSP" extends="SequenceFeature"
>                  is-interface="true">
>                        <reference name="blastHit"
>         referenced-type="BlastHit"/>
>                      </class>
>                  </classes>
>
>
>                  My Error
>                  =======
>
>                  BUILD FAILED
>
>         /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
>                  following error occurred while executing this line:
>                  /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201:
>                  Exception
>                  while reading from:
>
>         /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
>                  at
>
>         org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
>                  at
>
>         org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>                  at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>         Source)
>                  at
>
>         sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>                  at java.lang.reflect.Method.invoke(Method.java:606)
>                  at
>
>         org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>                  at org.apache.tools.ant.Task.perform(Task.java:348)
>                  at org.apache.tools.ant.Target.execute(Target.java:435)
>                  at
>         org.apache.tools.ant.Target.performTasks(Target.java:456)
>                  at
>
>         org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>                  at
>
>         org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>                  at
>         org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>                  at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
>                  at
>         org.intermine.task.Integrate.performAction(Integrate.java:223)
>                  at
>         org.intermine.task.Integrate.performAction(Integrate.java:135)
>                  at org.intermine.task.Integrate.execute(Integrate.java:127)
>                  at
>
>         org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>                  at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>         Source)
>                  at
>
>         sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>                  at java.lang.reflect.Method.invoke(Method.java:606)
>                  at
>
>         org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>                  at org.apache.tools.ant.Task.perform(Task.java:348)
>                  at org.apache.tools.ant.Target.execute(Target.java:435)
>                  at
>         org.apache.tools.ant.Target.performTasks(Target.java:456)
>                  at
>
>         org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>                  at
>         org.apache.tools.ant.Project.executeTarget(Project.java:1364)
>                  at
>
>         org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>                  at
>         org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>                  at org.apache.tools.ant.Main.runBuild(Main.java:851)
>                  at org.apache.tools.ant.Main.startAnt(Main.java:235)
>                  at
>         org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>                  at
>         org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>                  Caused by: org.intermine.InterMineException: Error during
>                  unmarshalling
>                  at
>         org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
>                  at
>
>         org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
>                  at
>
>         org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
>                  ... 31 more
>                  Caused by: java.lang.NullPointerException
>                  at java.lang.Class.isAssignableFrom(Native Method)
>                  at
>
>         org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
>                  at
>
>         org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
>                  at
>
>         org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
>                  at
>         org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
>                  ... 33 more
>
>                  Total time: 14 seconds
>
>
>                  _______________________________________________
>                  dev mailing list
>         [hidden email] <mailto:[hidden email]>
>         <mailto:[hidden email] <mailto:[hidden email]>>
>         http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Sofia Robb
Ok! I got it. Let me see if I can get it to work.

Thanks!
Sofia

On Fri, Oct 30, 2015 at 11:28 AM, Julie Sullivan <[hidden email]> wrote:


On 30/10/15 15:15, Sofia Robb wrote:
Do the reference items need to have the same name field as in the model?

Yes. The object you are storing has to match an object in the data model.

I that that as long as the type was the same, it was ok. Also, if I want
to have two organism references, both have to be in my model?

Yes. Everything you want to put in the database has to be in your model.

If your script is on github or somewhere public, I can try to help. :)

Julie

Thank you for your help,
Sofia

On Fri, Oct 30, 2015 at 11:07 AM, Julie Sullivan <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi Sofia,

    1. The Perl API will do a lot of things for you, like create the XML.

    2. Yes, you are right. Extending SequenceFeature will cause your
    object, BlastHSP, to inherit all it's references and collections.

    Specifically I was referring to these references in BlastHSP that
    are in the items XML:

    >         <reference name="BlastHitItem" ref_id="6_1" />
    >         <reference name="HitOrganismItem" ref_id="0_1" />
    >         <reference name="HitBioentityItem" ref_id="3_1" />
    >         <reference name="QueryOrganismItem" ref_id="0_0" />
    >         <reference name="QueryBioentityItem" ref_id="3_2" />

    They are not in your additions.xml.


    On 30/10/15 15:03, Sofia Robb wrote:

        Hi Julie,

        If you mean my own perl script when you say by hand, then yes. I
        thought
        that if I use the extend '<class name="BlastHSP"
        extends="SequenceFeature" is-interface="true">' that I could use
        whatever fields that this class can use.  Is this not true? I
        removed
        the name field in the reference items in all collections. This
        still did
        not help. I will explore the perl API.

        Thank you,
        Sofia

        On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan
        <[hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

             Hi Sofia!

             Sorry you are having problems.

             1. The additions file you give doesn't have the whole
        model. e.g.
             BlastHSP has fields in your items XML that aren't listed in
        your
             additions.

             Maybe because they are somewhere else in your model?

             2. The XML is formatted incorrectly, e.g. here:

                      <collection name="DataSources">
                              <reference name="DataSourceItem"
        ref_id="1_0" />
                              <reference name="DataSourceItem"
        ref_id="1_1" />
                      </collection>

             Should be something like:

                      <collection name="DataSources">
                              <reference ref_id="1_0" />
                              <reference ref_id="1_1" />
                      </collection>

             Although I don't know if that's what's causing your problems.

             3. I am guessing you are making the XML by hand. I do know some
             people who do this but most people use the Java or Perl API. It
             makes life easier! :)

        http://intermine.readthedocs.org/en/latest/database/data-sources/apis/

             Make the above fix and try again (be sure to use the -v tag
        in your
             command too if you aren't already), and let me know if that
        doesn't
             work.

             Julie


             On 29/10/15 19:37, Sofia Robb wrote:

                 Hi,

                 I am trying to write a blast intermine xml. I am
        getting errors when
                 loading it. Does anyone see what I am doing wrong?

                 Thank you,
                 Sofia

                 my Intermine xml
                 =============
                 <items>
                 <item id="1_0" class="DataSource">
                 <attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
                 <reference name="OrganismItem" ref_id="1_0" />
                 </item>
                 <item id="1_1" class="DataSource">
                 <attribute name="name"
        value="uniprot_sprot.fasta_2015_08"/>
                 </item>
                 <item id="2_0" class="DataSet">
                 <attribute name="name"
                 value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
                 <collection name="DataSources">
                 <reference name="DataSourceItem" ref_id="1_0" />
                 <reference name="DataSourceItem" ref_id="1_1" />
                 </collection>
                 </item>
                 <item id="5_1" class="BlastResult">
                 <attribute name="queryName"

        value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                 <attribute name="database" value="Uniprot_Swissprot"/>
                 <attribute name="algorithm" value="blastx"/>
                 <collection name="DataSources">
                 <reference name="DataSourceItem" ref_id="1_0" />
                 <reference name="DataSourceItem" ref_id="1_1" />
                 </collection>
                 <reference name="QueryOrganismItem" ref_id="0_0" />
                 </item>
                 <item id="6_1" class="BlastHit">
                 <attribute name="primaryIdentifier"
        value="sp|O19071|MGAT2_PIG"/>
                 <attribute name="score" value="7e-12"/>
                 <attribute name="scoreType" value="BlastHit_evalue"/>
                 <attribute name="description"
        value="Alpha-1,6-mannosyl-glycoprotein
                 2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa
        GN=MGAT2
                 PE=3 SV=1"/>
                 <reference name="BlastResultItem" ref_id="5_1" />
                 </item>
                 <item id="7_1" class="BlastHSP">
                 <attribute name="score" value="7e-12"/>
                 <attribute name="scoreType" value="BlastHSP_evalue"/>
                 <reference name="BlastHitItem" ref_id="6_1" />
                 <reference name="HitOrganismItem" ref_id="0_1" />
                 <reference name="HitBioentityItem" ref_id="3_1" />
                 <reference name="QueryOrganismItem" ref_id="0_0" />
                 <reference name="QueryBioentityItem" ref_id="3_2" />
                 </item>
                 <item id="4_2" class="Location">
                 <attribute name="start" value="3"/>
                 <attribute name="end" value="59"/>
                 <attribute name="strand" value="+"/>
                 <reference name="locatedOn" ref_id="3_2" />
                 </item>
                 <item id="4_1" class="Location">
                 <attribute name="start" value="338"/>
                 <attribute name="end" value="356"/>
                 <attribute name="strand" value="+"/>
                 <reference name="locatedOn" ref_id="3_1" />
                 </item>
                 <item id="0_0" class="Organism">
                 <attribute name="genus" value="Schmidtea"/>
                 <attribute name="species" value="mediterranea "/>
                 <attribute name="taxonId" value="79327"/>
                 <attribute name="commonName" value="Freshwater
        planarian flatworm"/>
                 </item>
                 <item id="0_1" class="Organism">
                 <attribute name="genus" value="Sus"/>
                 <attribute name="species" value="scrofa "/>
                 <attribute name="taxonId" value="9823"/>
                 <attribute name="commonName" value="Pig"/>
                 </item>
                 <item id="3_1" class="BioEntity">
                 <attribute name="name" value="sp|O19071|MGAT2_PIG"/>
                 <attribute name="primaryIdentifier"
        value="sp|O19071|MGAT2_PIG"/>
                 <reference name="organism" ref_id="0_1" />
                 </item>
                 <item id="3_2" class="BioEntity">
                 <attribute name="name"
        value="mk5-SmedSxl-v31.033737-0.1-1"/>
                 <attribute name="primaryIdentifier"
                 value="mk5-SmedSxl-v31.033737-0.1-1"/>
                 <attribute name="secondaryIdentifier"
                 value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                 <reference name="organism" ref_id="0_0" />
                 </item>
                 </items>

                 My blast_additions.xml
                 ======================
                 <classes>
                 <!-- add any <class> elements here -->
                     <class name="BlastResult" is-interface="true" >
                       <attribute name="queryName" type="java.lang.String"/>
                       <attribute name="database" type="java.lang.String"/>
                       <attribute name="algorithm" type="java.lang.String"/>
                       <collection name="DataSources"
        referenced-type="DataSource" />
                       <reference name="QueryOrganismItem"
                 referenced-type="Organism" />
                     </class>
                     <class name="BlastHit" extends="Gene"
        is-interface="true">
                       <reference name="blastResult"
        referenced-type="BlastResult" />
                     </class>
                     <class name="BlastHSP" extends="SequenceFeature"
                 is-interface="true">
                       <reference name="blastHit"
        referenced-type="BlastHit"/>
                     </class>
                 </classes>


                 My Error
                 =======

                 BUILD FAILED

        /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
                 following error occurred while executing this line:
                 /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201:
                 Exception
                 while reading from:

        /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
                 at

        org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
                 at

        org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
                 at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
        Source)
                 at

        sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                 at java.lang.reflect.Method.invoke(Method.java:606)
                 at

        org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
                 at org.apache.tools.ant.Task.perform(Task.java:348)
                 at org.apache.tools.ant.Target.execute(Target.java:435)
                 at
        org.apache.tools.ant.Target.performTasks(Target.java:456)
                 at

        org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
                 at

        org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
                 at
        org.apache.tools.ant.Project.executeTargets(Project.java:1248)
                 at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
                 at
        org.intermine.task.Integrate.performAction(Integrate.java:223)
                 at
        org.intermine.task.Integrate.performAction(Integrate.java:135)
                 at org.intermine.task.Integrate.execute(Integrate.java:127)
                 at

        org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
                 at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
        Source)
                 at

        sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                 at java.lang.reflect.Method.invoke(Method.java:606)
                 at

        org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
                 at org.apache.tools.ant.Task.perform(Task.java:348)
                 at org.apache.tools.ant.Target.execute(Target.java:435)
                 at
        org.apache.tools.ant.Target.performTasks(Target.java:456)
                 at

        org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
                 at
        org.apache.tools.ant.Project.executeTarget(Project.java:1364)
                 at

        org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
                 at
        org.apache.tools.ant.Project.executeTargets(Project.java:1248)
                 at org.apache.tools.ant.Main.runBuild(Main.java:851)
                 at org.apache.tools.ant.Main.startAnt(Main.java:235)
                 at
        org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
                 at
        org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
                 Caused by: org.intermine.InterMineException: Error during
                 unmarshalling
                 at
        org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
                 at

        org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
                 at

        org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
                 ... 31 more
                 Caused by: java.lang.NullPointerException
                 at java.lang.Class.isAssignableFrom(Native Method)
                 at

        org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
                 at

        org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
                 at

        org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
                 at
        org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
                 ... 33 more

                 Total time: 14 seconds


                 _______________________________________________
                 dev mailing list
        [hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>
        http://mail.intermine.org/cgi-bin/mailman/listinfo/dev





_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Sofia Robb
Ok! I got it to work when I was using my source as a type=>intermine-items-xml-file.

But my file is pretty big and i run out of memory, so changed my source to have the type => intermine-items-large-xml-file and I get the following error. What am I missing now?

Caused by: org.intermine.metadata.MetaDataException: Reference not found in class: BlastResult.QueryOrganismItem while translating Item with identifier 5_1

Thank you very much!
Sofia


here are  my additions file again and the item the error is referring to.

items
=====
        <item id="5_1" class="BlastResult">
                <attribute name="queryName" value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                <attribute name="database" value="Uniprot_Swissprot"/>
                <attribute name="algorithm" value="blastx"/>
                <collection name="dataSets">
                        <reference ref_id="2_0" />
                        <reference ref_id="2_1" />
                </collection>
                <reference name="QueryOrganismItem" ref_id="0_0" />
        </item>
        <item id="0_0" class="Organism">
                <attribute name="genus" value="Schmidtea"/>
                <attribute name="species" value="mediterranea "/>
                <attribute name="taxonId" value="79327"/>
                <attribute name="commonName" value="Freshwater planarian flatworm"/>
        </item>


additions file
==========
<classes>
<!-- add any <class> elements here -->
  <class name="BlastResult" is-interface="true" >
    <attribute name="queryName" type="java.lang.String"/>
    <attribute name="database" type="java.lang.String"/>
    <attribute name="algorithm" type="java.lang.String"/>
    <collection name="dataSets" referenced-type="DataSet" />
    <reference name="QueryOrganismItem" referenced-type="Organism" />
  </class>
  <class name="BlastHit" extends="Gene" is-interface="true">
    <reference name="BlastResultItem" referenced-type="BlastResult" />
  </class>
  <class name="BlastHSP" extends="SequenceFeature" is-interface="true">
    <!-- <reference name="blastHit" referenced-type="BlastHit"/> -->
    <reference name="BlastHitItem" referenced-type="BlastHit" />
    <reference name="HitOrganismItem" referenced-type="Organism" />
    <reference name="HitBioentityItem" referenced-type="BioEntity" />
    <reference name="HitLocationItem" referenced-type="Location" />
    <reference name="QueryOrganismItem" referenced-type="Organism" />
    <reference name="QueryBioentityItem" referenced-type="BioEntity" />
    <reference name="QueryLocationItem" referenced-type="Location" />
  </class>
</classes>


On Fri, Oct 30, 2015 at 11:30 AM, Sofia Robb <[hidden email]> wrote:
Ok! I got it. Let me see if I can get it to work.

Thanks!
Sofia

On Fri, Oct 30, 2015 at 11:28 AM, Julie Sullivan <[hidden email]> wrote:


On 30/10/15 15:15, Sofia Robb wrote:
Do the reference items need to have the same name field as in the model?

Yes. The object you are storing has to match an object in the data model.

I that that as long as the type was the same, it was ok. Also, if I want
to have two organism references, both have to be in my model?

Yes. Everything you want to put in the database has to be in your model.

If your script is on github or somewhere public, I can try to help. :)

Julie

Thank you for your help,
Sofia

On Fri, Oct 30, 2015 at 11:07 AM, Julie Sullivan <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi Sofia,

    1. The Perl API will do a lot of things for you, like create the XML.

    2. Yes, you are right. Extending SequenceFeature will cause your
    object, BlastHSP, to inherit all it's references and collections.

    Specifically I was referring to these references in BlastHSP that
    are in the items XML:

    >         <reference name="BlastHitItem" ref_id="6_1" />
    >         <reference name="HitOrganismItem" ref_id="0_1" />
    >         <reference name="HitBioentityItem" ref_id="3_1" />
    >         <reference name="QueryOrganismItem" ref_id="0_0" />
    >         <reference name="QueryBioentityItem" ref_id="3_2" />

    They are not in your additions.xml.


    On 30/10/15 15:03, Sofia Robb wrote:

        Hi Julie,

        If you mean my own perl script when you say by hand, then yes. I
        thought
        that if I use the extend '<class name="BlastHSP"
        extends="SequenceFeature" is-interface="true">' that I could use
        whatever fields that this class can use.  Is this not true? I
        removed
        the name field in the reference items in all collections. This
        still did
        not help. I will explore the perl API.

        Thank you,
        Sofia

        On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan
        <[hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

             Hi Sofia!

             Sorry you are having problems.

             1. The additions file you give doesn't have the whole
        model. e.g.
             BlastHSP has fields in your items XML that aren't listed in
        your
             additions.

             Maybe because they are somewhere else in your model?

             2. The XML is formatted incorrectly, e.g. here:

                      <collection name="DataSources">
                              <reference name="DataSourceItem"
        ref_id="1_0" />
                              <reference name="DataSourceItem"
        ref_id="1_1" />
                      </collection>

             Should be something like:

                      <collection name="DataSources">
                              <reference ref_id="1_0" />
                              <reference ref_id="1_1" />
                      </collection>

             Although I don't know if that's what's causing your problems.

             3. I am guessing you are making the XML by hand. I do know some
             people who do this but most people use the Java or Perl API. It
             makes life easier! :)

        http://intermine.readthedocs.org/en/latest/database/data-sources/apis/

             Make the above fix and try again (be sure to use the -v tag
        in your
             command too if you aren't already), and let me know if that
        doesn't
             work.

             Julie


             On 29/10/15 19:37, Sofia Robb wrote:

                 Hi,

                 I am trying to write a blast intermine xml. I am
        getting errors when
                 loading it. Does anyone see what I am doing wrong?

                 Thank you,
                 Sofia

                 my Intermine xml
                 =============
                 <items>
                 <item id="1_0" class="DataSource">
                 <attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
                 <reference name="OrganismItem" ref_id="1_0" />
                 </item>
                 <item id="1_1" class="DataSource">
                 <attribute name="name"
        value="uniprot_sprot.fasta_2015_08"/>
                 </item>
                 <item id="2_0" class="DataSet">
                 <attribute name="name"
                 value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
                 <collection name="DataSources">
                 <reference name="DataSourceItem" ref_id="1_0" />
                 <reference name="DataSourceItem" ref_id="1_1" />
                 </collection>
                 </item>
                 <item id="5_1" class="BlastResult">
                 <attribute name="queryName"

        value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                 <attribute name="database" value="Uniprot_Swissprot"/>
                 <attribute name="algorithm" value="blastx"/>
                 <collection name="DataSources">
                 <reference name="DataSourceItem" ref_id="1_0" />
                 <reference name="DataSourceItem" ref_id="1_1" />
                 </collection>
                 <reference name="QueryOrganismItem" ref_id="0_0" />
                 </item>
                 <item id="6_1" class="BlastHit">
                 <attribute name="primaryIdentifier"
        value="sp|O19071|MGAT2_PIG"/>
                 <attribute name="score" value="7e-12"/>
                 <attribute name="scoreType" value="BlastHit_evalue"/>
                 <attribute name="description"
        value="Alpha-1,6-mannosyl-glycoprotein
                 2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa
        GN=MGAT2
                 PE=3 SV=1"/>
                 <reference name="BlastResultItem" ref_id="5_1" />
                 </item>
                 <item id="7_1" class="BlastHSP">
                 <attribute name="score" value="7e-12"/>
                 <attribute name="scoreType" value="BlastHSP_evalue"/>
                 <reference name="BlastHitItem" ref_id="6_1" />
                 <reference name="HitOrganismItem" ref_id="0_1" />
                 <reference name="HitBioentityItem" ref_id="3_1" />
                 <reference name="QueryOrganismItem" ref_id="0_0" />
                 <reference name="QueryBioentityItem" ref_id="3_2" />
                 </item>
                 <item id="4_2" class="Location">
                 <attribute name="start" value="3"/>
                 <attribute name="end" value="59"/>
                 <attribute name="strand" value="+"/>
                 <reference name="locatedOn" ref_id="3_2" />
                 </item>
                 <item id="4_1" class="Location">
                 <attribute name="start" value="338"/>
                 <attribute name="end" value="356"/>
                 <attribute name="strand" value="+"/>
                 <reference name="locatedOn" ref_id="3_1" />
                 </item>
                 <item id="0_0" class="Organism">
                 <attribute name="genus" value="Schmidtea"/>
                 <attribute name="species" value="mediterranea "/>
                 <attribute name="taxonId" value="79327"/>
                 <attribute name="commonName" value="Freshwater
        planarian flatworm"/>
                 </item>
                 <item id="0_1" class="Organism">
                 <attribute name="genus" value="Sus"/>
                 <attribute name="species" value="scrofa "/>
                 <attribute name="taxonId" value="9823"/>
                 <attribute name="commonName" value="Pig"/>
                 </item>
                 <item id="3_1" class="BioEntity">
                 <attribute name="name" value="sp|O19071|MGAT2_PIG"/>
                 <attribute name="primaryIdentifier"
        value="sp|O19071|MGAT2_PIG"/>
                 <reference name="organism" ref_id="0_1" />
                 </item>
                 <item id="3_2" class="BioEntity">
                 <attribute name="name"
        value="mk5-SmedSxl-v31.033737-0.1-1"/>
                 <attribute name="primaryIdentifier"
                 value="mk5-SmedSxl-v31.033737-0.1-1"/>
                 <attribute name="secondaryIdentifier"
                 value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                 <reference name="organism" ref_id="0_0" />
                 </item>
                 </items>

                 My blast_additions.xml
                 ======================
                 <classes>
                 <!-- add any <class> elements here -->
                     <class name="BlastResult" is-interface="true" >
                       <attribute name="queryName" type="java.lang.String"/>
                       <attribute name="database" type="java.lang.String"/>
                       <attribute name="algorithm" type="java.lang.String"/>
                       <collection name="DataSources"
        referenced-type="DataSource" />
                       <reference name="QueryOrganismItem"
                 referenced-type="Organism" />
                     </class>
                     <class name="BlastHit" extends="Gene"
        is-interface="true">
                       <reference name="blastResult"
        referenced-type="BlastResult" />
                     </class>
                     <class name="BlastHSP" extends="SequenceFeature"
                 is-interface="true">
                       <reference name="blastHit"
        referenced-type="BlastHit"/>
                     </class>
                 </classes>


                 My Error
                 =======

                 BUILD FAILED

        /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
                 following error occurred while executing this line:
                 /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201:
                 Exception
                 while reading from:

        /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
                 at

        org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
                 at

        org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
                 at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
        Source)
                 at

        sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                 at java.lang.reflect.Method.invoke(Method.java:606)
                 at

        org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
                 at org.apache.tools.ant.Task.perform(Task.java:348)
                 at org.apache.tools.ant.Target.execute(Target.java:435)
                 at
        org.apache.tools.ant.Target.performTasks(Target.java:456)
                 at

        org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
                 at

        org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
                 at
        org.apache.tools.ant.Project.executeTargets(Project.java:1248)
                 at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
                 at
        org.intermine.task.Integrate.performAction(Integrate.java:223)
                 at
        org.intermine.task.Integrate.performAction(Integrate.java:135)
                 at org.intermine.task.Integrate.execute(Integrate.java:127)
                 at

        org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
                 at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
        Source)
                 at

        sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                 at java.lang.reflect.Method.invoke(Method.java:606)
                 at

        org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
                 at org.apache.tools.ant.Task.perform(Task.java:348)
                 at org.apache.tools.ant.Target.execute(Target.java:435)
                 at
        org.apache.tools.ant.Target.performTasks(Target.java:456)
                 at

        org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
                 at
        org.apache.tools.ant.Project.executeTarget(Project.java:1364)
                 at

        org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
                 at
        org.apache.tools.ant.Project.executeTargets(Project.java:1248)
                 at org.apache.tools.ant.Main.runBuild(Main.java:851)
                 at org.apache.tools.ant.Main.startAnt(Main.java:235)
                 at
        org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
                 at
        org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
                 Caused by: org.intermine.InterMineException: Error during
                 unmarshalling
                 at
        org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
                 at

        org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
                 at

        org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
                 ... 31 more
                 Caused by: java.lang.NullPointerException
                 at java.lang.Class.isAssignableFrom(Native Method)
                 at

        org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
                 at

        org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
                 at

        org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
                 at
        org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
                 ... 33 more

                 Total time: 14 seconds


                 _______________________________________________
                 dev mailing list
        [hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>
        http://mail.intermine.org/cgi-bin/mailman/listinfo/dev






_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Sofia Robb
Here is the full error:


BUILD FAILED
/var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The following error occurred while executing this line:
/var/lib/pgsql/other_data/intermine/imbuild/source.xml:330: java.lang.RuntimeException: ObjectStore error has occurred (in get)
at org.intermine.objectstore.query.Results.get(Results.java:233)
at org.intermine.objectstore.query.Results$Iter.hasNext(Results.java:378)
at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:135)
at org.intermine.dataloader.ObjectStoreDataLoader.process(ObjectStoreDataLoader.java:60)
at org.intermine.dataloader.ObjectStoreDataLoaderTask.execute(ObjectStoreDataLoaderTask.java:128)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
at org.intermine.task.Integrate.performAction(Integrate.java:223)
at org.intermine.task.Integrate.performAction(Integrate.java:136)
at org.intermine.task.Integrate.execute(Integrate.java:127)
at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown Source)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:606)
at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
at org.apache.tools.ant.Task.perform(Task.java:348)
at org.apache.tools.ant.Target.execute(Target.java:435)
at org.apache.tools.ant.Target.performTasks(Target.java:456)
at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
at org.apache.tools.ant.Project.executeTarget(Project.java:1364)
at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
at org.apache.tools.ant.Project.executeTargets(Project.java:1248)
at org.apache.tools.ant.Main.runBuild(Main.java:851)
at org.apache.tools.ant.Main.startAnt(Main.java:235)
at org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
at org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
Caused by: org.intermine.objectstore.ObjectStoreException: org.intermine.metadata.MetaDataException: Reference not found in class: BlastResult.QueryOrganismItem while translating Item with identifier 5_1
at org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.execute(ObjectStoreTranslatingImpl.java:168)
at org.intermine.objectstore.fastcollections.ObjectStoreFastCollectionsForTranslatorImpl.execute(ObjectStoreFastCollectionsForTranslatorImpl.java:197)
at org.intermine.dataloader.BatchingFetcher$NoseyObjectStore.execute(BatchingFetcher.java:559)
at org.intermine.objectstore.query.ResultsBatches.fetchBatchFromObjectStore(ResultsBatches.java:192)
at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:240)
at org.intermine.objectstore.query.PrefetchManager.doRequest(PrefetchManager.java:145)
at org.intermine.objectstore.query.ResultsBatches.getBatch(ResultsBatches.java:164)
at org.intermine.objectstore.query.ResultsBatches.getRowsFromBatch(ResultsBatches.java:139)
at org.intermine.objectstore.query.Results.range(Results.java:197)
at org.intermine.objectstore.query.SingletonResults.range(SingletonResults.java:65)
at org.intermine.objectstore.query.Results.get(Results.java:226)
... 35 more
Caused by: org.intermine.metadata.MetaDataException: Reference not found in class: BlastResult.QueryOrganismItem while translating Item with identifier 5_1
at org.intermine.dataconversion.ItemToObjectTranslator.translateFromDbObject(ItemToObjectTranslator.java:372)
at org.intermine.objectstore.translating.ObjectStoreTranslatingImpl.execute(ObjectStoreTranslatingImpl.java:155)
... 45 more

Total time: 18 seconds

On Fri, Oct 30, 2015 at 1:48 PM, Sofia Robb <[hidden email]> wrote:
Ok! I got it to work when I was using my source as a type=>intermine-items-xml-file.

But my file is pretty big and i run out of memory, so changed my source to have the type => intermine-items-large-xml-file and I get the following error. What am I missing now?

Caused by: org.intermine.metadata.MetaDataException: Reference not found in class: BlastResult.QueryOrganismItem while translating Item with identifier 5_1

Thank you very much!
Sofia


here are  my additions file again and the item the error is referring to.

items
=====
        <item id="5_1" class="BlastResult">
                <attribute name="queryName" value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                <attribute name="database" value="Uniprot_Swissprot"/>
                <attribute name="algorithm" value="blastx"/>
                <collection name="dataSets">
                        <reference ref_id="2_0" />
                        <reference ref_id="2_1" />
                </collection>
                <reference name="QueryOrganismItem" ref_id="0_0" />
        </item>
        <item id="0_0" class="Organism">
                <attribute name="genus" value="Schmidtea"/>
                <attribute name="species" value="mediterranea "/>
                <attribute name="taxonId" value="79327"/>
                <attribute name="commonName" value="Freshwater planarian flatworm"/>
        </item>


additions file
==========
<classes>
<!-- add any <class> elements here -->
  <class name="BlastResult" is-interface="true" >
    <attribute name="queryName" type="java.lang.String"/>
    <attribute name="database" type="java.lang.String"/>
    <attribute name="algorithm" type="java.lang.String"/>
    <collection name="dataSets" referenced-type="DataSet" />
    <reference name="QueryOrganismItem" referenced-type="Organism" />
  </class>
  <class name="BlastHit" extends="Gene" is-interface="true">
    <reference name="BlastResultItem" referenced-type="BlastResult" />
  </class>
  <class name="BlastHSP" extends="SequenceFeature" is-interface="true">
    <!-- <reference name="blastHit" referenced-type="BlastHit"/> -->
    <reference name="BlastHitItem" referenced-type="BlastHit" />
    <reference name="HitOrganismItem" referenced-type="Organism" />
    <reference name="HitBioentityItem" referenced-type="BioEntity" />
    <reference name="HitLocationItem" referenced-type="Location" />
    <reference name="QueryOrganismItem" referenced-type="Organism" />
    <reference name="QueryBioentityItem" referenced-type="BioEntity" />
    <reference name="QueryLocationItem" referenced-type="Location" />
  </class>
</classes>


On Fri, Oct 30, 2015 at 11:30 AM, Sofia Robb <[hidden email]> wrote:
Ok! I got it. Let me see if I can get it to work.

Thanks!
Sofia

On Fri, Oct 30, 2015 at 11:28 AM, Julie Sullivan <[hidden email]> wrote:


On 30/10/15 15:15, Sofia Robb wrote:
Do the reference items need to have the same name field as in the model?

Yes. The object you are storing has to match an object in the data model.

I that that as long as the type was the same, it was ok. Also, if I want
to have two organism references, both have to be in my model?

Yes. Everything you want to put in the database has to be in your model.

If your script is on github or somewhere public, I can try to help. :)

Julie

Thank you for your help,
Sofia

On Fri, Oct 30, 2015 at 11:07 AM, Julie Sullivan <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi Sofia,

    1. The Perl API will do a lot of things for you, like create the XML.

    2. Yes, you are right. Extending SequenceFeature will cause your
    object, BlastHSP, to inherit all it's references and collections.

    Specifically I was referring to these references in BlastHSP that
    are in the items XML:

    >         <reference name="BlastHitItem" ref_id="6_1" />
    >         <reference name="HitOrganismItem" ref_id="0_1" />
    >         <reference name="HitBioentityItem" ref_id="3_1" />
    >         <reference name="QueryOrganismItem" ref_id="0_0" />
    >         <reference name="QueryBioentityItem" ref_id="3_2" />

    They are not in your additions.xml.


    On 30/10/15 15:03, Sofia Robb wrote:

        Hi Julie,

        If you mean my own perl script when you say by hand, then yes. I
        thought
        that if I use the extend '<class name="BlastHSP"
        extends="SequenceFeature" is-interface="true">' that I could use
        whatever fields that this class can use.  Is this not true? I
        removed
        the name field in the reference items in all collections. This
        still did
        not help. I will explore the perl API.

        Thank you,
        Sofia

        On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan
        <[hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

             Hi Sofia!

             Sorry you are having problems.

             1. The additions file you give doesn't have the whole
        model. e.g.
             BlastHSP has fields in your items XML that aren't listed in
        your
             additions.

             Maybe because they are somewhere else in your model?

             2. The XML is formatted incorrectly, e.g. here:

                      <collection name="DataSources">
                              <reference name="DataSourceItem"
        ref_id="1_0" />
                              <reference name="DataSourceItem"
        ref_id="1_1" />
                      </collection>

             Should be something like:

                      <collection name="DataSources">
                              <reference ref_id="1_0" />
                              <reference ref_id="1_1" />
                      </collection>

             Although I don't know if that's what's causing your problems.

             3. I am guessing you are making the XML by hand. I do know some
             people who do this but most people use the Java or Perl API. It
             makes life easier! :)

        http://intermine.readthedocs.org/en/latest/database/data-sources/apis/

             Make the above fix and try again (be sure to use the -v tag
        in your
             command too if you aren't already), and let me know if that
        doesn't
             work.

             Julie


             On 29/10/15 19:37, Sofia Robb wrote:

                 Hi,

                 I am trying to write a blast intermine xml. I am
        getting errors when
                 loading it. Does anyone see what I am doing wrong?

                 Thank you,
                 Sofia

                 my Intermine xml
                 =============
                 <items>
                 <item id="1_0" class="DataSource">
                 <attribute name="name" value="SmedSxl_v3.1_MAKER_082015"/>
                 <reference name="OrganismItem" ref_id="1_0" />
                 </item>
                 <item id="1_1" class="DataSource">
                 <attribute name="name"
        value="uniprot_sprot.fasta_2015_08"/>
                 </item>
                 <item id="2_0" class="DataSet">
                 <attribute name="name"
                 value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
                 <collection name="DataSources">
                 <reference name="DataSourceItem" ref_id="1_0" />
                 <reference name="DataSourceItem" ref_id="1_1" />
                 </collection>
                 </item>
                 <item id="5_1" class="BlastResult">
                 <attribute name="queryName"

        value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                 <attribute name="database" value="Uniprot_Swissprot"/>
                 <attribute name="algorithm" value="blastx"/>
                 <collection name="DataSources">
                 <reference name="DataSourceItem" ref_id="1_0" />
                 <reference name="DataSourceItem" ref_id="1_1" />
                 </collection>
                 <reference name="QueryOrganismItem" ref_id="0_0" />
                 </item>
                 <item id="6_1" class="BlastHit">
                 <attribute name="primaryIdentifier"
        value="sp|O19071|MGAT2_PIG"/>
                 <attribute name="score" value="7e-12"/>
                 <attribute name="scoreType" value="BlastHit_evalue"/>
                 <attribute name="description"
        value="Alpha-1,6-mannosyl-glycoprotein
                 2-beta-N-acetylglucosaminyltransferase OS=Sus scrofa
        GN=MGAT2
                 PE=3 SV=1"/>
                 <reference name="BlastResultItem" ref_id="5_1" />
                 </item>
                 <item id="7_1" class="BlastHSP">
                 <attribute name="score" value="7e-12"/>
                 <attribute name="scoreType" value="BlastHSP_evalue"/>
                 <reference name="BlastHitItem" ref_id="6_1" />
                 <reference name="HitOrganismItem" ref_id="0_1" />
                 <reference name="HitBioentityItem" ref_id="3_1" />
                 <reference name="QueryOrganismItem" ref_id="0_0" />
                 <reference name="QueryBioentityItem" ref_id="3_2" />
                 </item>
                 <item id="4_2" class="Location">
                 <attribute name="start" value="3"/>
                 <attribute name="end" value="59"/>
                 <attribute name="strand" value="+"/>
                 <reference name="locatedOn" ref_id="3_2" />
                 </item>
                 <item id="4_1" class="Location">
                 <attribute name="start" value="338"/>
                 <attribute name="end" value="356"/>
                 <attribute name="strand" value="+"/>
                 <reference name="locatedOn" ref_id="3_1" />
                 </item>
                 <item id="0_0" class="Organism">
                 <attribute name="genus" value="Schmidtea"/>
                 <attribute name="species" value="mediterranea "/>
                 <attribute name="taxonId" value="79327"/>
                 <attribute name="commonName" value="Freshwater
        planarian flatworm"/>
                 </item>
                 <item id="0_1" class="Organism">
                 <attribute name="genus" value="Sus"/>
                 <attribute name="species" value="scrofa "/>
                 <attribute name="taxonId" value="9823"/>
                 <attribute name="commonName" value="Pig"/>
                 </item>
                 <item id="3_1" class="BioEntity">
                 <attribute name="name" value="sp|O19071|MGAT2_PIG"/>
                 <attribute name="primaryIdentifier"
        value="sp|O19071|MGAT2_PIG"/>
                 <reference name="organism" ref_id="0_1" />
                 </item>
                 <item id="3_2" class="BioEntity">
                 <attribute name="name"
        value="mk5-SmedSxl-v31.033737-0.1-1"/>
                 <attribute name="primaryIdentifier"
                 value="mk5-SmedSxl-v31.033737-0.1-1"/>
                 <attribute name="secondaryIdentifier"
                 value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                 <reference name="organism" ref_id="0_0" />
                 </item>
                 </items>

                 My blast_additions.xml
                 ======================
                 <classes>
                 <!-- add any <class> elements here -->
                     <class name="BlastResult" is-interface="true" >
                       <attribute name="queryName" type="java.lang.String"/>
                       <attribute name="database" type="java.lang.String"/>
                       <attribute name="algorithm" type="java.lang.String"/>
                       <collection name="DataSources"
        referenced-type="DataSource" />
                       <reference name="QueryOrganismItem"
                 referenced-type="Organism" />
                     </class>
                     <class name="BlastHit" extends="Gene"
        is-interface="true">
                       <reference name="blastResult"
        referenced-type="BlastResult" />
                     </class>
                     <class name="BlastHSP" extends="SequenceFeature"
                 is-interface="true">
                       <reference name="blastHit"
        referenced-type="BlastHit"/>
                     </class>
                 </classes>


                 My Error
                 =======

                 BUILD FAILED

        /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
                 following error occurred while executing this line:
                 /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201:
                 Exception
                 while reading from:

        /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
                 at

        org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
                 at

        org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
                 at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
        Source)
                 at

        sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                 at java.lang.reflect.Method.invoke(Method.java:606)
                 at

        org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
                 at org.apache.tools.ant.Task.perform(Task.java:348)
                 at org.apache.tools.ant.Target.execute(Target.java:435)
                 at
        org.apache.tools.ant.Target.performTasks(Target.java:456)
                 at

        org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
                 at

        org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
                 at
        org.apache.tools.ant.Project.executeTargets(Project.java:1248)
                 at org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
                 at
        org.intermine.task.Integrate.performAction(Integrate.java:223)
                 at
        org.intermine.task.Integrate.performAction(Integrate.java:135)
                 at org.intermine.task.Integrate.execute(Integrate.java:127)
                 at

        org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
                 at sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
        Source)
                 at

        sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                 at java.lang.reflect.Method.invoke(Method.java:606)
                 at

        org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
                 at org.apache.tools.ant.Task.perform(Task.java:348)
                 at org.apache.tools.ant.Target.execute(Target.java:435)
                 at
        org.apache.tools.ant.Target.performTasks(Target.java:456)
                 at

        org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
                 at
        org.apache.tools.ant.Project.executeTarget(Project.java:1364)
                 at

        org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
                 at
        org.apache.tools.ant.Project.executeTargets(Project.java:1248)
                 at org.apache.tools.ant.Main.runBuild(Main.java:851)
                 at org.apache.tools.ant.Main.startAnt(Main.java:235)
                 at
        org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
                 at
        org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
                 Caused by: org.intermine.InterMineException: Error during
                 unmarshalling
                 at
        org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
                 at

        org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
                 at

        org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
                 ... 31 more
                 Caused by: java.lang.NullPointerException
                 at java.lang.Class.isAssignableFrom(Native Method)
                 at

        org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
                 at

        org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
                 at

        org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
                 at
        org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
                 ... 33 more

                 Total time: 14 seconds


                 _______________________________________________
                 dev mailing list
        [hidden email] <mailto:[hidden email]>
        <mailto:[hidden email] <mailto:[hidden email]>>
        http://mail.intermine.org/cgi-bin/mailman/listinfo/dev







_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Julie Sullivan
In reply to this post by Sofia Robb
Hi Sofia!

Everything you have looks right to me. Have you tried an "ant clean"
first? It might be you are still working off of the old data model files
where BlastResult did not have an organism reference. Running the
"clean" target will remove the old files.

Try that?
Julie

On 30/10/15 17:48, Sofia Robb wrote:

> Ok! I got it to work when I was using my source as a
> type=>intermine-items-xml-file.
>
> But my file is pretty big and i run out of memory, so changed my source
> to have the type => intermine-items-large-xml-file and I get the
> following error. What am I missing now?
>
> Caused by: org.intermine.metadata.MetaDataException: Reference not found
> in class: BlastResult.QueryOrganismItem while translating Item with
> identifier 5_1
>
> Thank you very much!
> Sofia
>
>
> here are  my additions file again and the item the error is referring to.
>
> items
> =====
>          <item id="5_1" class="BlastResult">
>                  <attribute name="queryName"
> value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
>                  <attribute name="database" value="Uniprot_Swissprot"/>
>                  <attribute name="algorithm" value="blastx"/>
>                  <collection name="dataSets">
>                          <reference ref_id="2_0" />
>                          <reference ref_id="2_1" />
>                  </collection>
>                  <reference name="QueryOrganismItem" ref_id="0_0" />
>          </item>
>          <item id="0_0" class="Organism">
>                  <attribute name="genus" value="Schmidtea"/>
>                  <attribute name="species" value="mediterranea "/>
>                  <attribute name="taxonId" value="79327"/>
>                  <attribute name="commonName" value="Freshwater
> planarian flatworm"/>
>          </item>
>
>
> additions file
> ==========
> <classes>
> <!-- add any <class> elements here -->
>    <class name="BlastResult" is-interface="true" >
>      <attribute name="queryName" type="java.lang.String"/>
>      <attribute name="database" type="java.lang.String"/>
>      <attribute name="algorithm" type="java.lang.String"/>
>      <collection name="dataSets" referenced-type="DataSet" />
>      <reference name="QueryOrganismItem" referenced-type="Organism" />
>    </class>
>    <class name="BlastHit" extends="Gene" is-interface="true">
>      <reference name="BlastResultItem" referenced-type="BlastResult" />
>    </class>
>    <class name="BlastHSP" extends="SequenceFeature" is-interface="true">
>      <!-- <reference name="blastHit" referenced-type="BlastHit"/> -->
>      <reference name="BlastHitItem" referenced-type="BlastHit" />
>      <reference name="HitOrganismItem" referenced-type="Organism" />
>      <reference name="HitBioentityItem" referenced-type="BioEntity" />
>      <reference name="HitLocationItem" referenced-type="Location" />
>      <reference name="QueryOrganismItem" referenced-type="Organism" />
>      <reference name="QueryBioentityItem" referenced-type="BioEntity" />
>      <reference name="QueryLocationItem" referenced-type="Location" />
>    </class>
> </classes>
>
>
> On Fri, Oct 30, 2015 at 11:30 AM, Sofia Robb <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Ok! I got it. Let me see if I can get it to work.
>
>     Thanks!
>     Sofia
>
>     On Fri, Oct 30, 2015 at 11:28 AM, Julie Sullivan <[hidden email]
>     <mailto:[hidden email]>> wrote:
>
>
>
>         On 30/10/15 15:15, Sofia Robb wrote:
>
>             Do the reference items need to have the same name field as
>             in the model?
>
>
>         Yes. The object you are storing has to match an object in the
>         data model.
>
>             I that that as long as the type was the same, it was ok.
>             Also, if I want
>             to have two organism references, both have to be in my model?
>
>
>         Yes. Everything you want to put in the database has to be in
>         your model.
>
>         If your script is on github or somewhere public, I can try to
>         help. :)
>
>         Julie
>
>             Thank you for your help,
>             Sofia
>
>             On Fri, Oct 30, 2015 at 11:07 AM, Julie Sullivan
>             <[hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>> wrote:
>
>                  Hi Sofia,
>
>                  1. The Perl API will do a lot of things for you, like
>             create the XML.
>
>                  2. Yes, you are right. Extending SequenceFeature will
>             cause your
>                  object, BlastHSP, to inherit all it's references and
>             collections.
>
>                  Specifically I was referring to these references in
>             BlastHSP that
>                  are in the items XML:
>
>                  >         <reference name="BlastHitItem" ref_id="6_1" />
>                  >         <reference name="HitOrganismItem" ref_id="0_1" />
>                  >         <reference name="HitBioentityItem"
>             ref_id="3_1" />
>                  >         <reference name="QueryOrganismItem"
>             ref_id="0_0" />
>                  >         <reference name="QueryBioentityItem"
>             ref_id="3_2" />
>
>                  They are not in your additions.xml.
>
>
>                  On 30/10/15 15:03, Sofia Robb wrote:
>
>                      Hi Julie,
>
>                      If you mean my own perl script when you say by
>             hand, then yes. I
>                      thought
>                      that if I use the extend '<class name="BlastHSP"
>                      extends="SequenceFeature" is-interface="true">'
>             that I could use
>                      whatever fields that this class can use.  Is this
>             not true? I
>                      removed
>                      the name field in the reference items in all
>             collections. This
>                      still did
>                      not help. I will explore the perl API.
>
>                      Thank you,
>                      Sofia
>
>                      On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan
>                      <[hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>
>                      <mailto:[hidden email]
>             <mailto:[hidden email]> <mailto:[hidden email]
>             <mailto:[hidden email]>>>> wrote:
>
>                           Hi Sofia!
>
>                           Sorry you are having problems.
>
>                           1. The additions file you give doesn't have
>             the whole
>                      model. e.g.
>                           BlastHSP has fields in your items XML that
>             aren't listed in
>                      your
>                           additions.
>
>                           Maybe because they are somewhere else in your
>             model?
>
>                           2. The XML is formatted incorrectly, e.g. here:
>
>                                    <collection name="DataSources">
>                                            <reference name="DataSourceItem"
>                      ref_id="1_0" />
>                                            <reference name="DataSourceItem"
>                      ref_id="1_1" />
>                                    </collection>
>
>                           Should be something like:
>
>                                    <collection name="DataSources">
>                                            <reference ref_id="1_0" />
>                                            <reference ref_id="1_1" />
>                                    </collection>
>
>                           Although I don't know if that's what's causing
>             your problems.
>
>                           3. I am guessing you are making the XML by
>             hand. I do know some
>                           people who do this but most people use the
>             Java or Perl API. It
>                           makes life easier! :)
>
>             http://intermine.readthedocs.org/en/latest/database/data-sources/apis/
>
>                           Make the above fix and try again (be sure to
>             use the -v tag
>                      in your
>                           command too if you aren't already), and let me
>             know if that
>                      doesn't
>                           work.
>
>                           Julie
>
>
>                           On 29/10/15 19:37, Sofia Robb wrote:
>
>                               Hi,
>
>                               I am trying to write a blast intermine
>             xml. I am
>                      getting errors when
>                               loading it. Does anyone see what I am
>             doing wrong?
>
>                               Thank you,
>                               Sofia
>
>                               my Intermine xml
>                               =============
>                               <items>
>                               <item id="1_0" class="DataSource">
>                               <attribute name="name"
>             value="SmedSxl_v3.1_MAKER_082015"/>
>                               <reference name="OrganismItem" ref_id="1_0" />
>                               </item>
>                               <item id="1_1" class="DataSource">
>                               <attribute name="name"
>                      value="uniprot_sprot.fasta_2015_08"/>
>                               </item>
>                               <item id="2_0" class="DataSet">
>                               <attribute name="name"
>                               value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
>                               <collection name="DataSources">
>                               <reference name="DataSourceItem"
>             ref_id="1_0" />
>                               <reference name="DataSourceItem"
>             ref_id="1_1" />
>                               </collection>
>                               </item>
>                               <item id="5_1" class="BlastResult">
>                               <attribute name="queryName"
>
>
>             value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
>                               <attribute name="database"
>             value="Uniprot_Swissprot"/>
>                               <attribute name="algorithm" value="blastx"/>
>                               <collection name="DataSources">
>                               <reference name="DataSourceItem"
>             ref_id="1_0" />
>                               <reference name="DataSourceItem"
>             ref_id="1_1" />
>                               </collection>
>                               <reference name="QueryOrganismItem"
>             ref_id="0_0" />
>                               </item>
>                               <item id="6_1" class="BlastHit">
>                               <attribute name="primaryIdentifier"
>                      value="sp|O19071|MGAT2_PIG"/>
>                               <attribute name="score" value="7e-12"/>
>                               <attribute name="scoreType"
>             value="BlastHit_evalue"/>
>                               <attribute name="description"
>                      value="Alpha-1,6-mannosyl-glycoprotein
>                               2-beta-N-acetylglucosaminyltransferase
>             OS=Sus scrofa
>                      GN=MGAT2
>                               PE=3 SV=1"/>
>                               <reference name="BlastResultItem"
>             ref_id="5_1" />
>                               </item>
>                               <item id="7_1" class="BlastHSP">
>                               <attribute name="score" value="7e-12"/>
>                               <attribute name="scoreType"
>             value="BlastHSP_evalue"/>
>                               <reference name="BlastHitItem" ref_id="6_1" />
>                               <reference name="HitOrganismItem"
>             ref_id="0_1" />
>                               <reference name="HitBioentityItem"
>             ref_id="3_1" />
>                               <reference name="QueryOrganismItem"
>             ref_id="0_0" />
>                               <reference name="QueryBioentityItem"
>             ref_id="3_2" />
>                               </item>
>                               <item id="4_2" class="Location">
>                               <attribute name="start" value="3"/>
>                               <attribute name="end" value="59"/>
>                               <attribute name="strand" value="+"/>
>                               <reference name="locatedOn" ref_id="3_2" />
>                               </item>
>                               <item id="4_1" class="Location">
>                               <attribute name="start" value="338"/>
>                               <attribute name="end" value="356"/>
>                               <attribute name="strand" value="+"/>
>                               <reference name="locatedOn" ref_id="3_1" />
>                               </item>
>                               <item id="0_0" class="Organism">
>                               <attribute name="genus" value="Schmidtea"/>
>                               <attribute name="species"
>             value="mediterranea "/>
>                               <attribute name="taxonId" value="79327"/>
>                               <attribute name="commonName" value="Freshwater
>                      planarian flatworm"/>
>                               </item>
>                               <item id="0_1" class="Organism">
>                               <attribute name="genus" value="Sus"/>
>                               <attribute name="species" value="scrofa "/>
>                               <attribute name="taxonId" value="9823"/>
>                               <attribute name="commonName" value="Pig"/>
>                               </item>
>                               <item id="3_1" class="BioEntity">
>                               <attribute name="name"
>             value="sp|O19071|MGAT2_PIG"/>
>                               <attribute name="primaryIdentifier"
>                      value="sp|O19071|MGAT2_PIG"/>
>                               <reference name="organism" ref_id="0_1" />
>                               </item>
>                               <item id="3_2" class="BioEntity">
>                               <attribute name="name"
>                      value="mk5-SmedSxl-v31.033737-0.1-1"/>
>                               <attribute name="primaryIdentifier"
>                               value="mk5-SmedSxl-v31.033737-0.1-1"/>
>                               <attribute name="secondaryIdentifier"
>
>               value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
>                               <reference name="organism" ref_id="0_0" />
>                               </item>
>                               </items>
>
>                               My blast_additions.xml
>                               ======================
>                               <classes>
>                               <!-- add any <class> elements here -->
>                                   <class name="BlastResult"
>             is-interface="true" >
>                                     <attribute name="queryName"
>             type="java.lang.String"/>
>                                     <attribute name="database"
>             type="java.lang.String"/>
>                                     <attribute name="algorithm"
>             type="java.lang.String"/>
>                                     <collection name="DataSources"
>                      referenced-type="DataSource" />
>                                     <reference name="QueryOrganismItem"
>                               referenced-type="Organism" />
>                                   </class>
>                                   <class name="BlastHit" extends="Gene"
>                      is-interface="true">
>                                     <reference name="blastResult"
>                      referenced-type="BlastResult" />
>                                   </class>
>                                   <class name="BlastHSP"
>             extends="SequenceFeature"
>                               is-interface="true">
>                                     <reference name="blastHit"
>                      referenced-type="BlastHit"/>
>                                   </class>
>                               </classes>
>
>
>                               My Error
>                               =======
>
>                               BUILD FAILED
>
>
>             /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
>                               following error occurred while executing
>             this line:
>
>               /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201:
>                               Exception
>                               while reading from:
>
>
>             /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
>                               at
>
>
>             org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
>                               at
>
>
>             org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>                               at
>             sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>                      Source)
>                               at
>
>
>             sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>                               at
>             java.lang.reflect.Method.invoke(Method.java:606)
>                               at
>
>
>             org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>                               at
>             org.apache.tools.ant.Task.perform(Task.java:348)
>                               at
>             org.apache.tools.ant.Target.execute(Target.java:435)
>                               at
>
>             org.apache.tools.ant.Target.performTasks(Target.java:456)
>                               at
>
>
>             org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>                               at
>
>
>             org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
>                               at
>
>             org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>                               at
>             org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
>                               at
>
>             org.intermine.task.Integrate.performAction(Integrate.java:223)
>                               at
>
>             org.intermine.task.Integrate.performAction(Integrate.java:135)
>                               at
>             org.intermine.task.Integrate.execute(Integrate.java:127)
>                               at
>
>
>             org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
>                               at
>             sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
>                      Source)
>                               at
>
>
>             sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>                               at
>             java.lang.reflect.Method.invoke(Method.java:606)
>                               at
>
>
>             org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
>                               at
>             org.apache.tools.ant.Task.perform(Task.java:348)
>                               at
>             org.apache.tools.ant.Target.execute(Target.java:435)
>                               at
>
>             org.apache.tools.ant.Target.performTasks(Target.java:456)
>                               at
>
>
>             org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
>                               at
>
>             org.apache.tools.ant.Project.executeTarget(Project.java:1364)
>                               at
>
>
>             org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
>                               at
>
>             org.apache.tools.ant.Project.executeTargets(Project.java:1248)
>                               at
>             org.apache.tools.ant.Main.runBuild(Main.java:851)
>                               at
>             org.apache.tools.ant.Main.startAnt(Main.java:235)
>                               at
>
>             org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
>                               at
>
>             org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
>                               Caused by:
>             org.intermine.InterMineException: Error during
>                               unmarshalling
>                               at
>
>             org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
>                               at
>
>
>             org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
>                               at
>
>
>             org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
>                               ... 31 more
>                               Caused by: java.lang.NullPointerException
>                               at java.lang.Class.isAssignableFrom(Native
>             Method)
>                               at
>
>
>             org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
>                               at
>
>
>             org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
>                               at
>
>
>             org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
>                               at
>
>             org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
>                               ... 33 more
>
>                               Total time: 14 seconds
>
>
>
>               _______________________________________________
>                               dev mailing list
>             [hidden email] <mailto:[hidden email]>
>             <mailto:[hidden email] <mailto:[hidden email]>>
>                      <mailto:[hidden email]
>             <mailto:[hidden email]> <mailto:[hidden email]
>             <mailto:[hidden email]>>>
>             http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
>
>
>
>
>

_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev
Reply | Threaded
Open this post in threaded view
|

Re: blast intermine xml

Sofia Robb
I tried that. I tried ant clean in my dbmodel and integrate directories after I remake my source as a intermine-items-large-xml-file. I tried the "cd ../dbmodel/ ; ant clean build-db". And I am still getting this Reference not found error when I try to load my xml. It is so weird, my xml and model works when my source is 'intermine-items-xml-file' but not 'intermine-items-large-xml-file' (cleaning and rebuilding after each change). I guess I can break up dataset into many small xml and load that way, but that is not idea.

Thank for you help getting my xml and model working!
Sofia



On Mon, Nov 2, 2015 at 2:29 AM, Julie Sullivan <[hidden email]> wrote:
Hi Sofia!

Everything you have looks right to me. Have you tried an "ant clean" first? It might be you are still working off of the old data model files where BlastResult did not have an organism reference. Running the "clean" target will remove the old files.

Try that?
Julie


On 30/10/15 17:48, Sofia Robb wrote:
Ok! I got it to work when I was using my source as a
type=>intermine-items-xml-file.

But my file is pretty big and i run out of memory, so changed my source
to have the type => intermine-items-large-xml-file and I get the
following error. What am I missing now?

Caused by: org.intermine.metadata.MetaDataException: Reference not found
in class: BlastResult.QueryOrganismItem while translating Item with
identifier 5_1

Thank you very much!
Sofia


here are  my additions file again and the item the error is referring to.

items
=====
         <item id="5_1" class="BlastResult">
                 <attribute name="queryName"
value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                 <attribute name="database" value="Uniprot_Swissprot"/>
                 <attribute name="algorithm" value="blastx"/>
                 <collection name="dataSets">
                         <reference ref_id="2_0" />
                         <reference ref_id="2_1" />
                 </collection>
                 <reference name="QueryOrganismItem" ref_id="0_0" />
         </item>
         <item id="0_0" class="Organism">
                 <attribute name="genus" value="Schmidtea"/>
                 <attribute name="species" value="mediterranea "/>
                 <attribute name="taxonId" value="79327"/>
                 <attribute name="commonName" value="Freshwater
planarian flatworm"/>
         </item>


additions file
==========
<classes>
<!-- add any <class> elements here -->
   <class name="BlastResult" is-interface="true" >
     <attribute name="queryName" type="java.lang.String"/>
     <attribute name="database" type="java.lang.String"/>
     <attribute name="algorithm" type="java.lang.String"/>
     <collection name="dataSets" referenced-type="DataSet" />
     <reference name="QueryOrganismItem" referenced-type="Organism" />
   </class>
   <class name="BlastHit" extends="Gene" is-interface="true">
     <reference name="BlastResultItem" referenced-type="BlastResult" />
   </class>
   <class name="BlastHSP" extends="SequenceFeature" is-interface="true">
     <!-- <reference name="blastHit" referenced-type="BlastHit"/> -->
     <reference name="BlastHitItem" referenced-type="BlastHit" />
     <reference name="HitOrganismItem" referenced-type="Organism" />
     <reference name="HitBioentityItem" referenced-type="BioEntity" />
     <reference name="HitLocationItem" referenced-type="Location" />
     <reference name="QueryOrganismItem" referenced-type="Organism" />
     <reference name="QueryBioentityItem" referenced-type="BioEntity" />
     <reference name="QueryLocationItem" referenced-type="Location" />
   </class>
</classes>


On Fri, Oct 30, 2015 at 11:30 AM, Sofia Robb <[hidden email]
<mailto:[hidden email]>> wrote:

    Ok! I got it. Let me see if I can get it to work.

    Thanks!
    Sofia

    On Fri, Oct 30, 2015 at 11:28 AM, Julie Sullivan <[hidden email]
    <mailto:[hidden email]>> wrote:



        On 30/10/15 15:15, Sofia Robb wrote:

            Do the reference items need to have the same name field as
            in the model?


        Yes. The object you are storing has to match an object in the
        data model.

            I that that as long as the type was the same, it was ok.
            Also, if I want
            to have two organism references, both have to be in my model?


        Yes. Everything you want to put in the database has to be in
        your model.

        If your script is on github or somewhere public, I can try to
        help. :)

        Julie

            Thank you for your help,
            Sofia

            On Fri, Oct 30, 2015 at 11:07 AM, Julie Sullivan
            <[hidden email] <mailto:[hidden email]>
            <mailto:[hidden email] <mailto:[hidden email]>>> wrote:

                 Hi Sofia,

                 1. The Perl API will do a lot of things for you, like
            create the XML.

                 2. Yes, you are right. Extending SequenceFeature will
            cause your
                 object, BlastHSP, to inherit all it's references and
            collections.

                 Specifically I was referring to these references in
            BlastHSP that
                 are in the items XML:

                 >         <reference name="BlastHitItem" ref_id="6_1" />
                 >         <reference name="HitOrganismItem" ref_id="0_1" />
                 >         <reference name="HitBioentityItem"
            ref_id="3_1" />
                 >         <reference name="QueryOrganismItem"
            ref_id="0_0" />
                 >         <reference name="QueryBioentityItem"
            ref_id="3_2" />

                 They are not in your additions.xml.


                 On 30/10/15 15:03, Sofia Robb wrote:

                     Hi Julie,

                     If you mean my own perl script when you say by
            hand, then yes. I
                     thought
                     that if I use the extend '<class name="BlastHSP"
                     extends="SequenceFeature" is-interface="true">'
            that I could use
                     whatever fields that this class can use.  Is this
            not true? I
                     removed
                     the name field in the reference items in all
            collections. This
                     still did
                     not help. I will explore the perl API.

                     Thank you,
                     Sofia

                     On Fri, Oct 30, 2015 at 4:49 AM, Julie Sullivan
                     <[hidden email] <mailto:[hidden email]>
            <mailto:[hidden email] <mailto:[hidden email]>>
                     <mailto:[hidden email]
            <mailto:[hidden email]> <mailto:[hidden email]
            <mailto:[hidden email]>>>> wrote:

                          Hi Sofia!

                          Sorry you are having problems.

                          1. The additions file you give doesn't have
            the whole
                     model. e.g.
                          BlastHSP has fields in your items XML that
            aren't listed in
                     your
                          additions.

                          Maybe because they are somewhere else in your
            model?

                          2. The XML is formatted incorrectly, e.g. here:

                                   <collection name="DataSources">
                                           <reference name="DataSourceItem"
                     ref_id="1_0" />
                                           <reference name="DataSourceItem"
                     ref_id="1_1" />
                                   </collection>

                          Should be something like:

                                   <collection name="DataSources">
                                           <reference ref_id="1_0" />
                                           <reference ref_id="1_1" />
                                   </collection>

                          Although I don't know if that's what's causing
            your problems.

                          3. I am guessing you are making the XML by
            hand. I do know some
                          people who do this but most people use the
            Java or Perl API. It
                          makes life easier! :)

            http://intermine.readthedocs.org/en/latest/database/data-sources/apis/

                          Make the above fix and try again (be sure to
            use the -v tag
                     in your
                          command too if you aren't already), and let me
            know if that
                     doesn't
                          work.

                          Julie


                          On 29/10/15 19:37, Sofia Robb wrote:

                              Hi,

                              I am trying to write a blast intermine
            xml. I am
                     getting errors when
                              loading it. Does anyone see what I am
            doing wrong?

                              Thank you,
                              Sofia

                              my Intermine xml
                              =============
                              <items>
                              <item id="1_0" class="DataSource">
                              <attribute name="name"
            value="SmedSxl_v3.1_MAKER_082015"/>
                              <reference name="OrganismItem" ref_id="1_0" />
                              </item>
                              <item id="1_1" class="DataSource">
                              <attribute name="name"
                     value="uniprot_sprot.fasta_2015_08"/>
                              </item>
                              <item id="2_0" class="DataSet">
                              <attribute name="name"
                              value="SmedSxl_v3.1_MAKER_082015_VS_uniprot"/>
                              <collection name="DataSources">
                              <reference name="DataSourceItem"
            ref_id="1_0" />
                              <reference name="DataSourceItem"
            ref_id="1_1" />
                              </collection>
                              </item>
                              <item id="5_1" class="BlastResult">
                              <attribute name="queryName"


            value="mk5-SmedSxl-v31.033737-0.1-1;maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                              <attribute name="database"
            value="Uniprot_Swissprot"/>
                              <attribute name="algorithm" value="blastx"/>
                              <collection name="DataSources">
                              <reference name="DataSourceItem"
            ref_id="1_0" />
                              <reference name="DataSourceItem"
            ref_id="1_1" />
                              </collection>
                              <reference name="QueryOrganismItem"
            ref_id="0_0" />
                              </item>
                              <item id="6_1" class="BlastHit">
                              <attribute name="primaryIdentifier"
                     value="sp|O19071|MGAT2_PIG"/>
                              <attribute name="score" value="7e-12"/>
                              <attribute name="scoreType"
            value="BlastHit_evalue"/>
                              <attribute name="description"
                     value="Alpha-1,6-mannosyl-glycoprotein
                              2-beta-N-acetylglucosaminyltransferase
            OS=Sus scrofa
                     GN=MGAT2
                              PE=3 SV=1"/>
                              <reference name="BlastResultItem"
            ref_id="5_1" />
                              </item>
                              <item id="7_1" class="BlastHSP">
                              <attribute name="score" value="7e-12"/>
                              <attribute name="scoreType"
            value="BlastHSP_evalue"/>
                              <reference name="BlastHitItem" ref_id="6_1" />
                              <reference name="HitOrganismItem"
            ref_id="0_1" />
                              <reference name="HitBioentityItem"
            ref_id="3_1" />
                              <reference name="QueryOrganismItem"
            ref_id="0_0" />
                              <reference name="QueryBioentityItem"
            ref_id="3_2" />
                              </item>
                              <item id="4_2" class="Location">
                              <attribute name="start" value="3"/>
                              <attribute name="end" value="59"/>
                              <attribute name="strand" value="+"/>
                              <reference name="locatedOn" ref_id="3_2" />
                              </item>
                              <item id="4_1" class="Location">
                              <attribute name="start" value="338"/>
                              <attribute name="end" value="356"/>
                              <attribute name="strand" value="+"/>
                              <reference name="locatedOn" ref_id="3_1" />
                              </item>
                              <item id="0_0" class="Organism">
                              <attribute name="genus" value="Schmidtea"/>
                              <attribute name="species"
            value="mediterranea "/>
                              <attribute name="taxonId" value="79327"/>
                              <attribute name="commonName" value="Freshwater
                     planarian flatworm"/>
                              </item>
                              <item id="0_1" class="Organism">
                              <attribute name="genus" value="Sus"/>
                              <attribute name="species" value="scrofa "/>
                              <attribute name="taxonId" value="9823"/>
                              <attribute name="commonName" value="Pig"/>
                              </item>
                              <item id="3_1" class="BioEntity">
                              <attribute name="name"
            value="sp|O19071|MGAT2_PIG"/>
                              <attribute name="primaryIdentifier"
                     value="sp|O19071|MGAT2_PIG"/>
                              <reference name="organism" ref_id="0_1" />
                              </item>
                              <item id="3_2" class="BioEntity">
                              <attribute name="name"
                     value="mk5-SmedSxl-v31.033737-0.1-1"/>
                              <attribute name="primaryIdentifier"
                              value="mk5-SmedSxl-v31.033737-0.1-1"/>
                              <attribute name="secondaryIdentifier"

              value="maker-v31.033737-snap-gene-0.1-mRNA-1"/>
                              <reference name="organism" ref_id="0_0" />
                              </item>
                              </items>

                              My blast_additions.xml
                              ======================
                              <classes>
                              <!-- add any <class> elements here -->
                                  <class name="BlastResult"
            is-interface="true" >
                                    <attribute name="queryName"
            type="java.lang.String"/>
                                    <attribute name="database"
            type="java.lang.String"/>
                                    <attribute name="algorithm"
            type="java.lang.String"/>
                                    <collection name="DataSources"
                     referenced-type="DataSource" />
                                    <reference name="QueryOrganismItem"
                              referenced-type="Organism" />
                                  </class>
                                  <class name="BlastHit" extends="Gene"
                     is-interface="true">
                                    <reference name="blastResult"
                     referenced-type="BlastResult" />
                                  </class>
                                  <class name="BlastHSP"
            extends="SequenceFeature"
                              is-interface="true">
                                    <reference name="blastHit"
                     referenced-type="BlastHit"/>
                                  </class>
                              </classes>


                              My Error
                              =======

                              BUILD FAILED


            /var/lib/pgsql/other_data/intermine/imbuild/integrate.xml:54: The
                              following error occurred while executing
            this line:

              /var/lib/pgsql/other_data/intermine/imbuild/source.xml:201:
                              Exception
                              while reading from:


            /data/organisms/planaria/Smed/SmedSxl/genome/v31/Swissprot_blast/test.intermine.xml
                              at


            org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:170)
                              at


            org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
                              at
            sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
                     Source)
                              at


            sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                              at
            java.lang.reflect.Method.invoke(Method.java:606)
                              at


            org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
                              at
            org.apache.tools.ant.Task.perform(Task.java:348)
                              at
            org.apache.tools.ant.Target.execute(Target.java:435)
                              at

            org.apache.tools.ant.Target.performTasks(Target.java:456)
                              at


            org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
                              at


            org.apache.tools.ant.helper.SingleCheckExecutor.executeTargets(SingleCheckExecutor.java:38)
                              at

            org.apache.tools.ant.Project.executeTargets(Project.java:1248)
                              at
            org.apache.tools.ant.taskdefs.Ant.execute(Ant.java:440)
                              at

            org.intermine.task.Integrate.performAction(Integrate.java:223)
                              at

            org.intermine.task.Integrate.performAction(Integrate.java:135)
                              at
            org.intermine.task.Integrate.execute(Integrate.java:127)
                              at


            org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:292)
                              at
            sun.reflect.GeneratedMethodAccessor4.invoke(Unknown
                     Source)
                              at


            sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
                              at
            java.lang.reflect.Method.invoke(Method.java:606)
                              at


            org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)
                              at
            org.apache.tools.ant.Task.perform(Task.java:348)
                              at
            org.apache.tools.ant.Target.execute(Target.java:435)
                              at

            org.apache.tools.ant.Target.performTasks(Target.java:456)
                              at


            org.apache.tools.ant.Project.executeSortedTargets(Project.java:1393)
                              at

            org.apache.tools.ant.Project.executeTarget(Project.java:1364)
                              at


            org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)
                              at

            org.apache.tools.ant.Project.executeTargets(Project.java:1248)
                              at
            org.apache.tools.ant.Main.runBuild(Main.java:851)
                              at
            org.apache.tools.ant.Main.startAnt(Main.java:235)
                              at

            org.apache.tools.ant.launch.Launcher.run(Launcher.java:280)
                              at

            org.apache.tools.ant.launch.Launcher.main(Launcher.java:109)
                              Caused by:
            org.intermine.InterMineException: Error during
                              unmarshalling
                              at

            org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:64)
                              at


            org.intermine.dataloader.XmlDataLoader.processXml(XmlDataLoader.java:68)
                              at


            org.intermine.dataloader.XmlDataLoaderTask.execute(XmlDataLoaderTask.java:160)
                              ... 31 more
                              Caused by: java.lang.NullPointerException
                              at java.lang.Class.isAssignableFrom(Native
            Method)
                              at


            org.intermine.xml.full.FullParser.populateObject(FullParser.java:213)
                              at


            org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:135)
                              at


            org.intermine.xml.full.FullParser.realiseObjects(FullParser.java:78)
                              at

            org.intermine.util.XmlBinding.unmarshal(XmlBinding.java:62)
                              ... 33 more

                              Total time: 14 seconds



              _______________________________________________
                              dev mailing list
            [hidden email] <mailto:[hidden email]>
            <mailto:[hidden email] <mailto:[hidden email]>>
                     <mailto:[hidden email]
            <mailto:[hidden email]> <mailto:[hidden email]
            <mailto:[hidden email]>>>
            http://mail.intermine.org/cgi-bin/mailman/listinfo/dev







_______________________________________________
dev mailing list
[hidden email]
http://mail.intermine.org/cgi-bin/mailman/listinfo/dev