Changeset 16561

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Timestamp:
29/08/08 10:30:32 (4 months ago)
Author:
contrino
Message:

modmine: in project.jsp changed order of coulumn displayed; now metadata is last source in project.xml

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

    r16341 r16561  
    1111 */ 
    1212 
     13import java.sql.Connection; 
     14import java.sql.ResultSet; 
     15import java.sql.SQLException; 
     16import java.sql.Statement; 
    1317import java.util.ArrayList; 
    1418import java.util.Arrays; 
    …… 
    2327import java.util.Map.Entry; 
    2428 
     29import org.apache.commons.collections.keyvalue.MultiKey; 
     30import org.apache.commons.collections.map.MultiKeyMap; 
     31import org.apache.commons.lang.StringUtils; 
     32import org.apache.log4j.Logger; 
     33import org.flymine.model.genomic.LocatedSequenceFeature; 
     34import org.flymine.model.genomic.Transcript; 
    2535import org.intermine.bio.util.OrganismData; 
    2636import org.intermine.metadata.ClassDescriptor; 
    …… 
    3545import org.intermine.xml.full.Reference; 
    3646import org.intermine.xml.full.ReferenceList; 
    37  
    38 import org.flymine.model.genomic.LocatedSequenceFeature; 
    39 import org.flymine.model.genomic.Transcript; 
    40  
    41 import java.sql.Connection; 
    42 import java.sql.ResultSet; 
    43 import java.sql.SQLException; 
    44 import java.sql.Statement; 
    45  
    46 import org.apache.commons.collections.keyvalue.MultiKey; 
    47 import org.apache.commons.collections.map.MultiKeyMap; 
    48 import org.apache.commons.lang.StringUtils; 
    49 import org.apache.log4j.Logger; 
    5047 
    5148/** 
    …… 
    12941291    /** 
    12951292     * Return some SQL that can be included in the WHERE part of query that restricts features 
    1296      * by organism.  "organism_id" mus be selected. 
     1293     * by organism.  "organism_id" must be selected. 
    12971294     * @return the SQL 
    12981295     */ 

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

    r16126 r16561  
    8383    protected String getExtraFeatureConstraint() { 
    8484        String queryList = forINclause(); 
    85  
    86 //        LOG.info("LISTA " + queryList); 
    8785 
    8886        return "cvterm.name = 'chromosome' OR cvterm.name = 'chromosome_arm' OR feature_id IN " 

  • trunk/modmine/project.xml

    r16114 r16561  
    77    <source name="modencode-static" type="intermine-items-xml-file" dump="true"> 
    88      <property name="src.data.file" location="resources/projects.xml"/> 
    9     </source> 
    10     <source name="modencode-metadata" type="chado-db"> 
    11       <property name="organisms" value="7227"/> 
    12       <property name="dataSourceName" value="modENCODE"/> 
    13       <property name="dataSetTitle" value="modENCODE submission"/> 
    14       <property name="source.db.name" value="modencode-metadata"/> 
    15       <property name="processors" 
    16                 value="org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor"/> 
    17       <property name="converter.class"  
    18                 value="org.intermine.bio.dataconversion.ChadoDBConverter"/> 
    199    </source> 
    2010    <source name="chado-db-flybase-dmel" type="chado-db" dump="true"> 
    …… 
    127117      <property name="src.data.file" location="build/publications.xml"/> 
    128118    </source> 
    129  
     119        <source name="modencode-metadata" type="chado-db"> 
     120            <property name="organisms" value="7227"/> 
     121            <property name="dataSourceName" value="modENCODE"/> 
     122            <property name="dataSetTitle" value="modENCODE submission"/> 
     123            <property name="source.db.name" value="modencode-metadata"/> 
     124            <property name="processors" 
     125                                value="org.intermine.bio.dataconversion.ModEncodeMetaDataProcessor"/> 
     126            <property name="converter.class" 
     127                                value="org.intermine.bio.dataconversion.ChadoDBConverter"/> 
     128    </source> 
    130129  </sources> 
    131130  <post-processing> 

  • trunk/modmine/webapp/resources/webapp/model/projects.jsp

    r16438 r16561  
    2222        <th>Title</th> 
    2323        <th>Principal Investigator</th> 
    24         <th>Labs</th> 
    2524        <th>Submissions</th> 
     25    <th>Labs</th> 
    2626    </tr> 
    2727    <c:forEach items="${labs}" var="item"> 
    …… 
    3535    </html:link> 
    3636            <td>${item.key.namePI} ${item.key.surnamePI} 
     37 
     38<%-- 
    3739            <td><c:forEach items="${item.value}" var="prov"> 
    3840                <html:link 
    …… 
    4244                <br> 
    4345            </c:forEach> 
     46            --%> 
     47             
    4448            <td> 
    4549            <c:forEach items="${counts}" var="nr"> 
    …… 
    6872                </c:when> 
    6973            </c:choose> 
     74             
     75                 <td><c:forEach items="${item.value}" var="prov"> 
     76        <html:link 
     77          href="/${WEB_PROPERTIES['webapp.path']}/objectDetails.do?id=${prov.id}"> 
     78 ${prov.name} 
     79    </html:link> 
     80        <br> 
     81      </c:forEach> 
     82             
     83             
    7084    </c:forEach> 
    7185    </tr>