Changeset 16560

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Timestamp:
28/08/08 14:52:28 (3 months ago)
Author:
kmr
Message:

Fixed ChadoDBConverterTest.

Files:

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  • trunk/bio/sources/chado-db/main/src/org/intermine/bio/dataconversion/FlyBaseModuleProcessor.java

    r16481 r16560  
    197197     * @throws SQLException if there is a database problem 
    198198     */ 
    199     private void createInsertionTempTable(Connection connection) throws SQLException { 
     199    protected void createInsertionTempTable(Connection connection) throws SQLException { 
    200200        String query = 
    201201            " CREATE TEMPORARY TABLE " + INSERTION_TEMP_TABLE_NAME 

  • trunk/bio/sources/chado-db/test/resources/ChadoDBConverterTest.xml

    r16457 r16560  
    66  <item id="14_2" class="http://www.flymine.org/model/genomic#Publication"> 
    77    <attribute name="pubMedId" value="8543160"/> 
     8  </item> 
     9  <item id="12_6" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
     10    <attribute name="primaryIdentifier" value="FBti0030675"/> 
     11    <attribute name="secondaryIdentifier" value="P{RS3r}CB-0697-3"/> 
     12    <attribute name="symbol" value="P{RS3r}CB-0697-3"/> 
     13    <reference name="chromosomeLocation" ref_id="15_8"/> 
     14    <reference name="organism" ref_id="1_1"/> 
     15    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    816  </item> 
    917  <item id="5_41" class="http://www.flymine.org/model/genomic#Synonym"> 
    …… 
    4149    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    4250  </item> 
    43   <item id="12_2" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
    44     <attribute name="name" value="P{RS3}CB-0697-3"/> 
    45     <attribute name="primaryIdentifier" value="FBti0028225"/> 
    46     <attribute name="symbol" value="P{RS3}CB-0697-3"/> 
    47     <reference name="organism" ref_id="1_1"/> 
    48     <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    49   </item> 
    5051  <item id="5_5" class="http://www.flymine.org/model/genomic#Synonym"> 
    5152    <attribute name="isPrimary" value="true"/> 
    …… 
    9091    <reference name="source" ref_id="3_1"/> 
    9192    <reference name="subject" ref_id="0_1"/> 
    92     <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    93   </item> 
    94   <item id="12_4" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
    95     <attribute name="name" value="P{RS5r}5-HA-1496"/> 
    96     <attribute name="primaryIdentifier" value="FBti0031976"/> 
    97     <attribute name="symbol" value="P{RS5r}5-HA-1496"/> 
    98     <reference name="chromosomeLocation" ref_id="15_10"/> 
    99     <reference name="organism" ref_id="1_1"/> 
    10093    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    10194  </item> 
    …… 
    174167    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    175168  </item> 
     169  <item id="12_5" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
     170    <attribute name="primaryIdentifier" value="FBti0030830"/> 
     171    <attribute name="secondaryIdentifier" value="P{RS3r}CB-5069-3"/> 
     172    <attribute name="symbol" value="P{RS3r}CB-5069-3"/> 
     173    <reference name="organism" ref_id="1_1"/> 
     174    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
     175  </item> 
    176176  <item id="15_4" class="http://www.flymine.org/model/genomic#Location"> 
    177177    <attribute name="end" value="24577107"/> 
    …… 
    198198  <item id="19_1" class="http://www.flymine.org/model/genomic#DevelopmentTerm"> 
    199199    <attribute name="identifier" value="FBdv:00005289"/> 
     200  </item> 
     201  <item id="12_1" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
     202    <attribute name="primaryIdentifier" value="FBti0028380"/> 
     203    <attribute name="secondaryIdentifier" value="P{RS3}CB-5069-3"/> 
     204    <attribute name="symbol" value="P{RS3}CB-5069-3"/> 
     205    <reference name="organism" ref_id="1_1"/> 
     206    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    200207  </item> 
    201208  <item id="0_1" class="http://www.flymine.org/model/genomic#Gene"> 
    …… 
    258265    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    259266  </item> 
     267  <item id="12_3" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
     268    <attribute name="primaryIdentifier" value="FBti0032815"/> 
     269    <attribute name="secondaryIdentifier" value="P{RS5r}5-SZ-4122"/> 
     270    <attribute name="symbol" value="P{RS5r}5-SZ-4122"/> 
     271    <reference name="chromosomeLocation" ref_id="15_9"/> 
     272    <reference name="organism" ref_id="1_1"/> 
     273    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
     274  </item> 
    260275  <item id="5_40" class="http://www.flymine.org/model/genomic#Synonym"> 
    261276    <attribute name="isPrimary" value="false"/> 
    …… 
    280295    <reference name="source" ref_id="3_1"/> 
    281296    <reference name="subject" ref_id="12_8"/> 
    282     <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    283   </item> 
    284   <item id="12_3" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
    285     <attribute name="name" value="P{RS5r}5-SZ-4122"/> 
    286     <attribute name="primaryIdentifier" value="FBti0032815"/> 
    287     <attribute name="symbol" value="P{RS5r}5-SZ-4122"/> 
    288     <reference name="chromosomeLocation" ref_id="15_9"/> 
    289     <reference name="organism" ref_id="1_1"/> 
    290297    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    291298  </item> 
    …… 
    341348    <reference name="source" ref_id="3_1"/> 
    342349    <reference name="subject" ref_id="12_3"/> 
    343     <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    344   </item> 
    345   <item id="12_7" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
    346     <attribute name="name" value="P{RS5}5-SZ-4122"/> 
    347     <attribute name="primaryIdentifier" value="FBti0030367"/> 
    348     <attribute name="symbol" value="P{RS5}5-SZ-4122"/> 
    349     <reference name="organism" ref_id="1_1"/> 
    350350    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    351351  </item> 
    …… 
    402402    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    403403  </item> 
     404  <item id="12_8" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
     405    <attribute name="primaryIdentifier" value="FBti0029528"/> 
     406    <attribute name="secondaryIdentifier" value="P{RS5}5-HA-1496"/> 
     407    <attribute name="symbol" value="P{RS5}5-HA-1496"/> 
     408    <reference name="organism" ref_id="1_1"/> 
     409    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
     410  </item> 
    404411  <item id="18_1" class="http://www.flymine.org/model/genomic#CVTerm"> 
    405412    <attribute name="identifier" value="FBcv:0000031"/> 
    …… 
    411418  <item id="14_6" class="http://www.flymine.org/model/genomic#Publication"> 
    412419    <attribute name="pubMedId" value="7772020"/> 
    413   </item> 
    414   <item id="12_5" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
    415     <attribute name="name" value="P{RS3r}CB-5069-3"/> 
    416     <attribute name="primaryIdentifier" value="FBti0030830"/> 
    417     <attribute name="symbol" value="P{RS3r}CB-5069-3"/> 
    418     <reference name="organism" ref_id="1_1"/> 
    419     <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    420420  </item> 
    421421  <item id="14_7" class="http://www.flymine.org/model/genomic#Publication"> 
    …… 
    449449    <attribute name="taxonId" value="7227"/> 
    450450  </item> 
    451   <item id="12_1" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
    452     <attribute name="name" value="P{RS3}CB-5069-3"/> 
    453     <attribute name="primaryIdentifier" value="FBti0028380"/> 
    454     <attribute name="symbol" value="P{RS3}CB-5069-3"/> 
    455     <reference name="organism" ref_id="1_1"/> 
    456     <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    457   </item> 
    458451  <item id="5_43" class="http://www.flymine.org/model/genomic#Synonym"> 
    459452    <attribute name="isPrimary" value="true"/> 
    …… 
    532525    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    533526  </item> 
    534   <item id="12_8" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
    535     <attribute name="name" value="P{RS5}5-HA-1496"/> 
    536     <attribute name="primaryIdentifier" value="FBti0029528"/> 
    537     <attribute name="symbol" value="P{RS5}5-HA-1496"/> 
    538     <reference name="organism" ref_id="1_1"/> 
    539     <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    540   </item> 
    541527  <item id="15_2" class="http://www.flymine.org/model/genomic#Location"> 
    542528    <attribute name="end" value="102000"/> 
    …… 
    545531    <reference name="object" ref_id="7_1"/> 
    546532    <reference name="subject" ref_id="0_1"/> 
     533    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
     534  </item> 
     535  <item id="12_7" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
     536    <attribute name="primaryIdentifier" value="FBti0030367"/> 
     537    <attribute name="secondaryIdentifier" value="P{RS5}5-SZ-4122"/> 
     538    <attribute name="symbol" value="P{RS5}5-SZ-4122"/> 
     539    <reference name="organism" ref_id="1_1"/> 
    547540    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    548541  </item> 
    …… 
    715708    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    716709  </item> 
     710  <item id="12_4" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
     711    <attribute name="primaryIdentifier" value="FBti0031976"/> 
     712    <attribute name="secondaryIdentifier" value="P{RS5r}5-HA-1496"/> 
     713    <attribute name="symbol" value="P{RS5r}5-HA-1496"/> 
     714    <reference name="chromosomeLocation" ref_id="15_10"/> 
     715    <reference name="organism" ref_id="1_1"/> 
     716    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
     717  </item> 
    717718  <item id="15_1" class="http://www.flymine.org/model/genomic#Location"> 
    718719    <attribute name="end" value="14990594"/> 
    …… 
    733734    <attribute name="identifier" value="FBcv:0000323"/> 
    734735  </item> 
     736  <item id="12_2" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
     737    <attribute name="primaryIdentifier" value="FBti0028225"/> 
     738    <attribute name="secondaryIdentifier" value="P{RS3}CB-0697-3"/> 
     739    <attribute name="symbol" value="P{RS3}CB-0697-3"/> 
     740    <reference name="organism" ref_id="1_1"/> 
     741    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
     742  </item> 
    735743  <item id="5_23" class="http://www.flymine.org/model/genomic#Synonym"> 
    736744    <attribute name="isPrimary" value="true"/> 
    …… 
    768776    <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    769777  </item> 
    770   <item id="12_6" class="http://www.flymine.org/model/genomic#TransposableElementInsertionSite"> 
    771     <attribute name="name" value="P{RS3r}CB-0697-3"/> 
    772     <attribute name="primaryIdentifier" value="FBti0030675"/> 
    773     <attribute name="symbol" value="P{RS3r}CB-0697-3"/> 
    774     <reference name="chromosomeLocation" ref_id="15_8"/> 
    775     <reference name="organism" ref_id="1_1"/> 
    776     <collection name="dataSets"><reference ref_id="4_1"/></collection> 
    777   </item> 
    778778</items> 

  • trunk/bio/sources/chado-db/test/src/org/intermine/bio/dataconversion/TestFlyBaseModuleProcessor.java

    r16457 r16560  
    2626public class TestFlyBaseModuleProcessor extends FlyBaseModuleProcessor 
    2727{ 
     28 
    2829    /** 
    2930     * Create a new TestFlyBaseModuleProcessor object. 
    …… 
    3940    @Override 
    4041    protected void createFeatureTempTable(@SuppressWarnings("unused") Connection connection) { 
     42        // empty 
     43    } 
     44 
     45    /** 
     46     * {@inheritDoc} 
     47     */ 
     48    @Override 
     49    protected void createInsertionTempTable(@SuppressWarnings("unused") Connection connection) { 
    4150        // empty 
    4251    }