Changeset 670


Ignore:
Timestamp:
Apr 18, 2008, 5:27:14 PM (14 years ago)
Author:
mbayer
Message:
  • build script tidied up
  • new BASE libs added and existing ones updated (2.6.2)
  • fixed compile errors and warnings caused by API changes in update 2.6.2
Location:
plugins/base2/uk.ac.ebi.tab2mage/branches/tab2mageimporter
Files:
2 added
1 deleted
9 edited

Legend:

Unmodified
Added
Removed
  • plugins/base2/uk.ac.ebi.tab2mage/branches/tab2mageimporter/build.xml

    r659 r670  
    33
    44  <!-- variables used -->
    5   <property name="src.plugins" location="src" />
    6   <property name="bin.plugins" location="bin" />
    7   <property name="lib.plugins" location="lib" />
    8   <property name="util.src.plugins" location="${src.plugins}/uk/ac/ebi/nugo/common/" />
    9   <property name="core.src.plugins" location="${src.plugins}/uk/ac/ebi/nugo/plugins" />
     5  <property name="src" location="src" />
     6  <property name="bin" location="bin" />
     7  <property name="lib" location="lib" />
     8  <property name="util" location="${src}/uk/ac/ebi/nugo/common/" />
     9  <property name="core" location="${src}/uk/ac/ebi/nugo/plugins" />
    1010
    11   <property name="plugin.name" value="Tab2MageImporter" />
    12   <property name="utils.name" value="ebi-plugins-utils" />
     11  <property name="pluginName" value="Tab2MageImporter" />
     12  <property name="utilsName" value="ebi-plugins-utils" />
    1313  <property name="jspDir" location="jsp" />
    1414 
    1515  <!-- tomcat -->
    1616  <property environment="env"/>
    17   <property name="tomcat.home" value="${env.CATALINA_HOME}" />
    18   <property name="tomcat.shutdownscript" value="${tomcat.home}/bin/shutdown.bat" />
    19   <property name="tomcat.startupscript" value="${tomcat.home}/bin/startup.bat" />
     17  <property name="tomcatHome" value="${env.CATALINA_HOME}" />
     18  <property name="tomcatShutdown" value="${tomcatHome}/bin/shutdown.bat" />
     19  <property name="tomcatStartup" value="${tomcatHome}/bin/startup.bat" />
    2020 
    2121
    2222  <!-- set up classpath for compiling -->
    23   <path id="nugo.plugin.compile.classpath">
    24     <fileset dir="${lib.plugins}">
     23  <path id="classpath">
     24    <fileset dir="${lib}">
    2525      <include name="**/*.jar" />
    2626    </fileset>
    2727  </path>
    2828
    29   <target name="build.plugin" depends="utils,plugin.compile" description="Compile the plugin" />
     29  <target name="buildAll" depends="utils,compile" description="Compile the plugin" />
    3030
    3131  <target name="utils" depends="clean" description="compile the common ebi -plugin util classes">
    32     <javac encoding="ISO-8859-1" srcdir="${util.src.plugins}" destdir="${bin.plugins}" classpathref="nugo.plugin.compile.classpath" debug="true" deprecation="true">
     32    <javac encoding="ISO-8859-1" srcdir="${util}" destdir="${bin}" classpathref="classpath" debug="true" deprecation="true">
    3333    </javac>
    34     <jar basedir="${bin.plugins}" jarfile="${lib.plugins}\ebi-plugins-utils.jar" />
    35     <jar basedir="${bin.plugins}" jarfile="${utils.name}.jar" />
     34    <jar basedir="${bin}" jarfile="${lib}\ebi-plugins-utils.jar" />
     35    <jar basedir="${bin}" jarfile="${utilsName}.jar" />
    3636    <delete includeemptydirs="true">
    37       <fileset dir="${bin.plugins}" includes="**/*" />
     37      <fileset dir="${bin}" includes="**/*" />
    3838    </delete>
    3939  </target>
    4040
    41   <target name="plugin.compile" depends="clean" description="compile the ta2mage importer plugin source code, without dependencies and put in a jar file">
     41  <target name="compile" depends="clean" description="compile the ta2mage importer plugin source code, without dependencies and put in a jar file">
    4242    <mkdir dir="bin"/>
    43     <javac source="1.5" target="1.5" encoding="ISO-8859-1" srcdir="${core.src.plugins}" destdir="${bin.plugins}" classpathref="nugo.plugin.compile.classpath" debug="true" deprecation="true">
     43    <javac source="1.6" target="1.6" encoding="ISO-8859-1" srcdir="${core}" destdir="${bin}" classpathref="classpath" debug="true" deprecation="true">
    4444    </javac>
    45     <jar basedir="${bin.plugins}" jarfile="${plugin.name}.jar" manifest="MANIFEST.MF" />
     45    <jar basedir="${bin}" jarfile="${pluginName}.jar" manifest="MANIFEST.MF" />
    4646    <delete includeemptydirs="true">
    47       <fileset dir="${bin.plugins}" includes="**/*" />
     47      <fileset dir="${bin}" includes="**/*" />
    4848    </delete>
    4949  </target>
    5050
    5151  <target name="all" depends="clean" description="compile all the ta2mage importer plugin source code with dependencies and put in a jar file">
    52     <javac source="1.5" target="1.5" encoding="ISO-8859-1" srcdir="${src.plugins}" destdir="${bin.plugins}" classpathref="nugo.plugin.compile.classpath" debug="true" deprecation="true">
     52    <javac source="1.5" target="1.5" encoding="ISO-8859-1" srcdir="${src}" destdir="${bin}" classpathref="classpath" debug="true" deprecation="true">
    5353    </javac>
    54     <jar basedir="${bin.plugins}" jarfile="${plugin.name}.jar" manifest="MANIFEST.MF" />
     54    <jar basedir="${bin}" jarfile="${pluginName}.jar" manifest="MANIFEST.MF" />
    5555  </target>
    5656
    5757  <target name="clean" depends="" description="clean/clear the bin folder">
    5858    <delete includeemptydirs="true">
    59       <fileset dir="${bin.plugins}" includes="**/*" />
     59      <fileset dir="${bin}" includes="**/*" />
    6060    </delete>
    6161  </target>
     
    6363
    6464  <target name="copyJSPs">
    65     <copy todir="${tomcat.home}\webapps\base\plugins\" verbose="false">
     65    <copy todir="${tomcatHome}\webapps\base\plugins\" verbose="false">
    6666      <fileset dir="${jspDir}" />
    6767    </copy>
     
    6969
    7070
    71   <target name="copyToServer" depends="build.plugin,copyJSPs">
    72     <copy file="${plugin.name}.jar" todir="${tomcat.home}\webapps\base\WEB-INF\lib" verbose="false" />
    73     <copy file="${utils.name}.jar" todir="${tomcat.home}\webapps\base\WEB-INF\lib" verbose="false" />
     71  <target name="copyToServer" depends="buildAll,copyJSPs">
     72    <copy file="${pluginName}.jar" todir="${tomcatHome}\webapps\base\WEB-INF\lib" verbose="false" />
     73    <copy file="${utilsName}.jar" todir="${tomcatHome}\webapps\base\WEB-INF\lib" verbose="false" />
    7474    <!-- now restart tomcat to reload the application -->
    7575    <echo message="tomcat home = "/>
    76     <echo message="${tomcat.home}"/>
     76    <echo message="${tomcatHome}"/>
    7777    <echo message="shutting down tomcat" />
    78     <exec executable="${tomcat.shutdownscript}" spawn="yes" />
     78    <exec executable="${tomcatShutdown}" spawn="yes" />
    7979    <echo message="starting up tomcat" />
    80     <exec executable="${tomcat.startupscript}" spawn="yes" />
     80    <exec executable="${tomcatStartup}" spawn="yes" />
    8181  </target>
    8282
  • plugins/base2/uk.ac.ebi.tab2mage/branches/tab2mageimporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/RawDataImport.java

    r471 r670  
    105105        if (dc ==null || dc.isClosed()) dc = sc.newDbControl();
    106106        RawBioAssay rba = RawBioAssay.getById(dc,rbas.getId());
    107         if (rba.hasData() || rba.getSpots()>=1)
     107        if (rba.hasData())
    108108        {
    109109          log.info("rba = " + rba.getName()+ " has data already");
  • plugins/base2/uk.ac.ebi.tab2mage/branches/tab2mageimporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/Tab2MageDataImportFactory.java

    r654 r670  
    1111
    1212import net.sf.basedb.core.Affymetrix;
     13import net.sf.basedb.core.DataFileType;
    1314import net.sf.basedb.core.DbControl;
    1415import net.sf.basedb.core.File;
     16import net.sf.basedb.core.FileStoreUtil;
    1517import net.sf.basedb.core.PluginConfiguration;
    1618import net.sf.basedb.core.ProgressReporter;
     
    145147            log.info("The file is: " + file.getName());
    146148            // need to attach the cel file to the bioassay object
    147             Affymetrix.setCelFile(rba, file);
     149            FileStoreUtil.setDataFile(dc, rba, DataFileType.AFFYMETRIX_CEL, file);
     150            //deprecated:
     151            //Affymetrix.setCelFile(rba, file);
    148152          }
    149153        }
  • plugins/base2/uk.ac.ebi.tab2mage/branches/tab2mageimporter/src/uk/ac/ebi/nugo/plugins/tab2mageimport/io/Tab2MageHybWriter.java

    r654 r670  
    2626import net.sf.basedb.core.Extract;
    2727import net.sf.basedb.core.Hybridization;
     28import net.sf.basedb.core.Include;
    2829import net.sf.basedb.core.InvalidDataException;
    2930import net.sf.basedb.core.Item;
     31import net.sf.basedb.core.ItemQuery;
    3032import net.sf.basedb.core.Label;
    3133import net.sf.basedb.core.LabeledExtract;
     34import net.sf.basedb.core.Platform;
    3235import net.sf.basedb.core.Protocol;
    3336import net.sf.basedb.core.RawBioAssay;
     
    6366   */
    6467  private ArrayList<Tab2MAGEHybridization> hybs=null;
    65 
     68 
    6669  /**
    6770    the database control
     
    7881 
    7982  private List<RawBioAssay> rbaCatche= new ArrayList<RawBioAssay>();
    80 
     83 
    8184  /**
    8285    The set of experimental factors
    8386   */
    8487  private Set<String> expFactors= new HashSet<String>();
    85 
     88 
    8689 
    8790  /**
     
    98101    this.dc= dc;
    99102    this.protocolAccessionMap = map;
    100  
     103   
    101104  }
    102105 
     
    117120   
    118121    if (!rbaCatche.isEmpty()) // clear the raw bio assay store data storage/catche
    119         rbaCatche.clear();
     122      rbaCatche.clear();
    120123    int i=0;
    121124    if (hybs!=null)     
     
    129132          i++;
    130133          for (Tab2MAGEHybridizationLine  hybLine : hyb.getLines())
    131               {
    132                 //clear the catche first, if not empty
     134          {
     135            //clear the catche first, if not empty
    133136            if (!protocolCatche.isEmpty())
    134137              protocolCatche.clear();
     
    137140            if (!factorValueCatche.isEmpty())
    138141              factorValueCatche.clear();
    139                        
     142           
    140143            //get all the protocol type - accession map for the hyb first
    141                 Map<String, String> protMap= hybLine.getProtocol();
    142                
    143                 //catche all the other protocols required (protocol type - accession map for the hyb).
    144                 protocolCatche = protMap;
    145        
    146                 // get all parameter for this hybline
    147                 Map<String, String> parameterMap = hybLine.getParameter();
    148                
    149                 //catche the hybline parameter for later use
    150                 parameterCatche = parameterMap;
    151                
    152                 // get all factor value for this hyb line
    153                 Map<String, String> factorMap = hybLine.getFactorValues();
    154                
    155                 // catche the hybline parameter for later use
    156                 factorValueCatche = factorMap;
    157                
    158                 // get experimental factors [AT]
    159                 for (Map.Entry<String, String> fact : factorMap.entrySet())
    160                 {
    161                   expFactors.add(fact.getKey());
    162                 }
    163                 // write Biosource
    164                 BioSource bio= createBioSource(hybLine.getBioSource(), bioSources, hybLine.getBioMaterialCharacteristics());
    165                
    166                 // write the samples
    167                 Sample sample= createSample(hybLine.getSample(), bio, samples, hybLine.getParameter(),protMap );
    168                
    169                 // write Extract             
    170                 Extract extract= createExtract(hybLine.getExtract(), sample, extracts, hybLine.getParameter(), protMap);
    171                
    172                 //write Labeled Extract
    173                 String dye = hybLine.getDye();
    174                 Label label =Helper.getLabel(dye, dc);
    175                 LabeledExtract lextract= createLabeledExtract(hybLine.getLabeledExtract(), dye, label, extract, lExtracts, hybLine.getParameter(), protMap);
    176                 // add lextract to a list of labeled extracts
    177                 labeledExtracts.add(lextract);
    178               } //end of Hybridization line
    179 
     144            Map<String, String> protMap= hybLine.getProtocol();
     145           
     146            //catche all the other protocols required (protocol type - accession map for the hyb).
     147            protocolCatche = protMap;
     148           
     149            // get all parameter for this hybline
     150            Map<String, String> parameterMap = hybLine.getParameter();
     151           
     152            //catche the hybline parameter for later use
     153            parameterCatche = parameterMap;
     154           
     155            // get all factor value for this hyb line
     156            Map<String, String> factorMap = hybLine.getFactorValues();
     157           
     158            // catche the hybline parameter for later use
     159            factorValueCatche = factorMap;
     160           
     161            // get experimental factors [AT]
     162            for (Map.Entry<String, String> fact : factorMap.entrySet())
     163            {
     164              expFactors.add(fact.getKey());
     165            }
     166            // write Biosource
     167            BioSource bio= createBioSource(hybLine.getBioSource(), bioSources, hybLine.getBioMaterialCharacteristics());
     168           
     169            // write the samples
     170            Sample sample= createSample(hybLine.getSample(), bio, samples, hybLine.getParameter(),protMap );
     171           
     172            // write Extract             
     173            Extract extract= createExtract(hybLine.getExtract(), sample, extracts, hybLine.getParameter(), protMap);
     174           
     175            //write Labeled Extract
     176            String dye = hybLine.getDye();
     177            Label label =Helper.getLabel(dye, dc);
     178            LabeledExtract lextract= createLabeledExtract(hybLine.getLabeledExtract(), dye, label, extract, lExtracts, hybLine.getParameter(), protMap);
     179            // add lextract to a list of labeled extracts
     180            labeledExtracts.add(lextract);
     181          } //end of Hybridization line
     182         
    180183          // get Array Design. Array Design must have been created by a user with administrative rights
    181               String accession=Tab2MageHelper.findTab2MageAccessionOrSerial(hyb.getArrayInformation(), "accession");
    182               ArrayDesign arrayDesign = Helper.getArrayDesign(accession,dc);
    183               if (arrayDesign==null)
    184               {
    185                 log.error("No Array Design was found in the BASE2. You would have to create this to run Tab2mage Importer");
    186                 return done=false;
    187               }
    188               dc.reattachItem(arrayDesign);
    189              
    190               // Create Array Batch
    191               ArrayBatch ab = createArrayBatch(arrayDesign, i);
    192              
    193               // Create Array Serial
    194               String slide =Tab2MageHelper.findTab2MageAccessionOrSerial(hyb.getArrayInformation(), "serial");
    195               ArraySlide arraySlide = getSlide(slide,ab, arrayDesign, i );
    196              
    197               //  write Hybridization
    198                 Hybridization newHyb = createHybridization(hyb.getName(), arraySlide, labeledExtracts, parameterCatche, protocolCatche);
    199              
    200               //write Scan
    201                 Scan scan = createScan( newHyb, parameterCatche, protocolCatche);
    202              
    203               //write Raw Bio Assay
    204                 RawBioAssay rba = createRawBioAssay(hyb.getFileRaw(), rdt, scan, arrayDesign, parameterCatche, protocolCatche, factorValueCatche);
    205                 rbaCatche.add(rba);
    206                 //log.debug("Raw Bio Assay"+ rba.getName()+ "is added to catch");
     184          String accession=Tab2MageHelper.findTab2MageAccessionOrSerial(hyb.getArrayInformation(), "accession");
     185          ArrayDesign arrayDesign = Helper.getArrayDesign(accession,dc);
     186          if (arrayDesign==null)
     187          {
     188            log.error("No Array Design was found in the BASE2. You would have to create this to run Tab2mage Importer");
     189            return done=false;
     190          }
     191          dc.reattachItem(arrayDesign);
     192         
     193          // Create Array Batch
     194          ArrayBatch ab = createArrayBatch(arrayDesign, i);
     195         
     196          // Create Array Serial
     197          String slide =Tab2MageHelper.findTab2MageAccessionOrSerial(hyb.getArrayInformation(), "serial");
     198          ArraySlide arraySlide = getSlide(slide,ab, arrayDesign, i );
     199         
     200          //  write Hybridization
     201          Hybridization newHyb = createHybridization(hyb.getName(), arraySlide, labeledExtracts, parameterCatche, protocolCatche);
     202         
     203          //write Scan
     204          Scan scan = createScan( newHyb, parameterCatche, protocolCatche);
     205         
     206          //write Raw Bio Assay
     207          RawBioAssay rba = createRawBioAssay(hyb.getFileRaw(), rdt, scan, arrayDesign, parameterCatche, protocolCatche, factorValueCatche);
     208          rbaCatche.add(rba);
     209          //log.debug("Raw Bio Assay"+ rba.getName()+ "is added to catch");
    207210        }// end of each Hyb
    208211      }
     
    247250      bio.setName(name);
    248251      // add the annotations for biomaterial characteristics
    249         try
    250         {
    251           setAnnotations(bio, xters);
    252         }
    253         catch (InvalidDataException ide)
    254         {
    255           log.warn("Annotation for BioMaterial Characteristics cannot be set. Check the allowed values for the annotation type");
    256         }
    257         dc.saveItem(bio);
    258         bioSources.put(bio.getName(),bio);
    259         log.info("--The biosource created is :" + bio.getName());
     252      try
     253      {
     254        setAnnotations(bio, xters);
     255      }
     256      catch (InvalidDataException ide)
     257      {
     258        log.warn("Annotation for BioMaterial Characteristics cannot be set. Check the allowed values for the annotation type");
     259      }
     260      dc.saveItem(bio);
     261      bioSources.put(bio.getName(),bio);
     262      log.info("--The biosource created is :" + bio.getName());
    260263    }
    261264    return bio;
     
    270273      @return
    271274   */
    272 
     275 
    273276  private Sample createSample(String name, BioSource biosource, Map<String, BasicItem> samples, Map<String, String> param, Map<String, String> protMap )
    274277  {
     
    285288      sample.setName(name);
    286289      sample.setBioSource(biosource);
    287         String sAccessionNo = getProtocolAccesion(protMap,"treatment");  //grow and treatment are the allowed protocol types speccfied in tab2mage specification
     290      String sAccessionNo = getProtocolAccesion(protMap,"treatment");  //grow and treatment are the allowed protocol types speccfied in tab2mage specification
    288291      if ("".equals(sAccessionNo))
    289         {
    290           sAccessionNo = getProtocolAccesion(protMap,"grow");
    291         }
    292         BioMaterialEvent sEvent= sample.getCreationEvent();
    293         sEvent.setProtocol(getProtocol(sAccessionNo));
    294         // add the  annotation for protocol parameters
    295         try
    296         {
    297           setParameterAnnotations(sample, param);
    298         }
    299         catch (InvalidDataException ide)
    300         {
    301           log.warn("Annotation for Sampling Protocol cannot be set. Check the allowed values for the annotation type");
    302         }
    303        
    304         // add the annotations for sample characteristics for MAGE-TAB
    305         dc.saveItem(sample);
    306         samples.put(sample.getName(),sample);
    307         log.info("--The sample created is :" + sample.getName()+"\n");
     292      {
     293        sAccessionNo = getProtocolAccesion(protMap,"grow");
     294      }
     295      BioMaterialEvent sEvent= sample.getCreationEvent();
     296      sEvent.setProtocol(getProtocol(sAccessionNo));
     297      // add the  annotation for protocol parameters
     298      try
     299      {
     300        setParameterAnnotations(sample, param);
     301      }
     302      catch (InvalidDataException ide)
     303      {
     304        log.warn("Annotation for Sampling Protocol cannot be set. Check the allowed values for the annotation type");
     305      }
     306     
     307      // add the annotations for sample characteristics for MAGE-TAB
     308      dc.saveItem(sample);
     309      samples.put(sample.getName(),sample);
     310      log.info("--The sample created is :" + sample.getName()+"\n");
    308311    }
    309312    return sample;
     
    329332    else
    330333    {
    331         extract = Extract.getNew(dc);
    332         extract.setName(name);
    333         extract.setSample(sample,  Float.parseFloat("0.10"));
    334        
    335         String eAccessionNo = getProtocolAccesion(protMap,"extraction"); //
    336         BioMaterialEvent eEvent= extract.getCreationEvent();
    337         eEvent.setProtocol(getProtocol(eAccessionNo));
    338         //  add the  annotation for protocol parameters
    339         try
    340         {
    341           setParameterAnnotations(extract, param);
    342         }
    343         catch (InvalidDataException ide)
    344         {
    345           log.warn("Annotation for Extraction Protocol cannot be set. Check the allowed values for the annotation type" + ide.getMessage());
    346         }
    347         // add the extract annotations for MAG- TAB sample characteristics
    348         dc.saveItem(extract);
    349         extracts.put(extract.getName(),extract);
    350         log.info("--The extract created is :" + extract.getName()+"\n");
     334      extract = Extract.getNew(dc);
     335      extract.setName(name);
     336      extract.setSample(sample,  Float.parseFloat("0.10"));
     337     
     338      String eAccessionNo = getProtocolAccesion(protMap,"extraction"); //
     339      BioMaterialEvent eEvent= extract.getCreationEvent();
     340      eEvent.setProtocol(getProtocol(eAccessionNo));
     341      //  add the  annotation for protocol parameters
     342      try
     343      {
     344        setParameterAnnotations(extract, param);
     345      }
     346      catch (InvalidDataException ide)
     347      {
     348        log.warn("Annotation for Extraction Protocol cannot be set. Check the allowed values for the annotation type" + ide.getMessage());
     349      }
     350      // add the extract annotations for MAG- TAB sample characteristics
     351      dc.saveItem(extract);
     352      extracts.put(extract.getName(),extract);
     353      log.info("--The extract created is :" + extract.getName()+"\n");
    351354    }
    352355    return extract;
     
    406409   */
    407410  private Hybridization createHybridization(String name, ArraySlide arraySlide,List<LabeledExtract> labeledExtracts,
    408       Map<String, String> parCatche, Map<String,String> proCatche )
     411          Map<String, String> parCatche, Map<String,String> proCatche )
    409412  {
    410413    log.info("--Creating hybridization: " + name + "\n");
     
    413416    newHyb.setName(name);
    414417    newHyb.setArraySlide(arraySlide );
    415                
     418   
    416419    BioMaterialEvent bioMaterialEvent= newHyb.getCreationEvent();
    417420    for (LabeledExtract lb :labeledExtracts )
     
    429432    {
    430433      log.warn("Annotation for Hybridization Protocol cannot be set. Check the allowed values for the annotation type in BASE");
    431 
     434     
    432435    }
    433436    dc.saveItem(newHyb);
     
    475478   */
    476479  private RawBioAssay createRawBioAssay( String name, RawDataType rawDataType, Scan scan, ArrayDesign arrayDesign,
    477       Map<String,String> parCatche, Map<String,String> protCatche, Map<String, String>factCatche)
     480          Map<String,String> parCatche, Map<String,String> protCatche, Map<String, String>factCatche)
    478481  {
    479482    log.info("--Creating raw bioassay: " + name +"\n");
    480       RawBioAssay rba = RawBioAssay.getNew(dc, rawDataType);
    481       rba.setName(name);
    482       rba.setScan(scan);
    483       if (!rba.hasArrayDesign()) rba.setArrayDesign(arrayDesign);
     483
     484    //get the platform object first   
     485    //make a query for all platform objects in the db
     486    ItemQuery<Platform> query = Platform.getQuery();
     487    query.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);   
     488    //check through them all to see if the raw datatype matches our raw datatype here
     489    Platform platform = null;
     490    for(Platform p : query.list(dc))
     491    {
     492      RawDataType queryRdt = p.getRawDataType();
     493      if(queryRdt.getName().equalsIgnoreCase(rawDataType.getName()))
     494      {
     495        platform = p;
     496        break;
     497      }
     498    }
     499   
     500    //now make a new raw bioassay
     501    RawBioAssay rba = RawBioAssay.getNew(dc, platform, rawDataType);
     502    rba.setName(name);
     503    rba.setScan(scan);
     504    if (!rba.hasArrayDesign()) rba.setArrayDesign(arrayDesign);
    484505    String accessionNo = getProtocolAccesion(protCatche,"feature extraction"); //could pass protocol type as parameter
    485506    rba.setProtocol(getProtocol(accessionNo));
     
    509530    return rba;
    510531  }
    511 
     532 
    512533  /**
    513534    obtains array slide matching the serial name in the tab2smage file.
     
    527548    return as;
    528549  }
    529    
     550 
    530551  /**
    531552    creates a new array batch if one does not exist already 
     
    568589  /**
    569590      get protocol given the protocolname and type
    570     * @return
    571     */
     591  * @return
     592  */
    572593  private Protocol getProtocol(String protocolAccesion)
    573594  {
     
    729750    return expFactors;
    730751  }
    731 
     752 
    732753}
    733754
    734        
     755
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