Changeset 6435


Ignore:
Timestamp:
Mar 17, 2014, 9:01:38 AM (9 years ago)
Author:
Nicklas Nordborg
Message:

References #1797: Deprecate web services

Most compilation warnings disappeared by not 'import'-ing the deprecated classes but using fully qualified class names instead. The rest of the warnings disappeared by adding @SuppressWarnings("deprecation") to the class definitions. This should be removed once the web services has been removed in #1798.

The WSDL generation issue was solved by adding jsr311-api.1.0.jar which contains the missing class. Seems like adding @Deprecated annotations to the web service classes triggered some extra checks which needed some more classes.

Location:
trunk
Files:
2 added
25 edited

Legend:

Unmodified
Added
Removed

  • trunk/src/core/net/sf/basedb/core/DynamicSpotQuery.java

    r6127 r6435  
    5959  @base.modified $Date$
    6060*/
     61@SuppressWarnings("deprecation")
    6162public class DynamicSpotQuery
    6263  extends DynamicQuery

  • trunk/src/core/net/sf/basedb/core/FileSet.java

    r6127 r6435  
    3434import net.sf.basedb.core.query.Hql;
    3535import net.sf.basedb.core.query.Restrictions;
    36 
    3736import net.sf.basedb.core.data.FileSetData;
    3837import net.sf.basedb.core.data.FileSetMemberData;
    … …  
    5554  @base.modified $Date$
    5655*/
     56@SuppressWarnings("deprecation")
    5757public class FileSet
    5858  extends BasicItem<FileSetData>

  • trunk/src/core/net/sf/basedb/core/ItemSubtype.java

    r6127 r6435  
    5050  @base.modified $Date$
    5151*/
     52@SuppressWarnings("deprecation")
    5253public class ItemSubtype
    5354  extends BasicItem<ItemSubtypeData>

  • trunk/src/core/net/sf/basedb/core/Job.java

    r6432 r6435  
    7575  @base.modified $Date$
    7676*/
     77@SuppressWarnings("deprecation")
    7778public class Job
    7879  extends OwnedItem<JobData>

  • trunk/src/core/net/sf/basedb/core/PluginDefinition.java

    r6127 r6435  
    6464  @base.modified $Date$
    6565*/
     66@SuppressWarnings("deprecation")
    6667public class PluginDefinition
    6768  extends CommonItem<PluginDefinitionData>

  • trunk/src/core/net/sf/basedb/core/Protocol.java

    r6127 r6435  
    3737  @version 2.0
    3838*/
     39@SuppressWarnings("deprecation")
    3940public class Protocol
    4041  extends AnnotatedItem<ProtocolData>

  • trunk/src/core/net/sf/basedb/core/RawDataType.java

    r6127 r6435  
    4545  @base.modified $Date$
    4646*/
     47@SuppressWarnings("deprecation")
    4748public class RawDataType
    4849  implements Comparable<RawDataType>

  • trunk/src/core/net/sf/basedb/core/SessionControl.java

    r6427 r6435  
    7575  @base.modified $Date$
    7676*/
     77@SuppressWarnings("deprecation")
    7778public class SessionControl
    7879{

  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/AnnotationTypeClient.java

    r6434 r6435  
    2222package net.sf.basedb.ws.client;
    2323
    24 import net.sf.basedb.info.AnnotationTypeInfo;
    25 import net.sf.basedb.info.QueryOptions;
    2624
    2725import org.apache.axis2.AxisFault;
    … …  
    5654      @throws AxisFault If communication with web service fails.
    5755  */
    58   public AnnotationTypeInfo getById(int itemId)
     56  public net.sf.basedb.info.AnnotationTypeInfo getById(int itemId)
    5957    throws AxisFault
    6058  {
    61     return invokeBlocking("getById", AnnotationTypeInfo.class,
     59    return invokeBlocking("getById", net.sf.basedb.info.AnnotationTypeInfo.class,
    6260      session.getId(), itemId);
    6361  }
    … …  
    7068      @throws AxisFault If communication with web service fails.
    7169   */
    72   public AnnotationTypeInfo[] getAnnotationTypes(String itemType, QueryOptions qOpt)
     70  public net.sf.basedb.info.AnnotationTypeInfo[] getAnnotationTypes(String itemType, net.sf.basedb.info.QueryOptions qOpt)
    7371    throws AxisFault
    7472  {   
    75     AnnotationTypeInfo[] result = invokeBlocking("getAnnotationTypes", AnnotationTypeInfo[].class,
     73    net.sf.basedb.info.AnnotationTypeInfo[] result = invokeBlocking("getAnnotationTypes", net.sf.basedb.info.AnnotationTypeInfo[].class,
    7674      session.getId(), itemType, qOpt);
    7775    return result;

  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/ArrayDesignClient.java

    r6434 r6435  
    2222package net.sf.basedb.ws.client;
    2323
    24 import net.sf.basedb.info.ArrayDesignInfo;
    25 import net.sf.basedb.info.DataFileTypeInfo;
    26 import net.sf.basedb.info.FileSetMemberInfo;
    27 import net.sf.basedb.info.QueryOptions;
    2824
    2925import java.io.IOException;
    … …  
    6662    @throws AxisFault If communication with web service fails.
    6763  */
    68   public ArrayDesignInfo getById(int itemId)
     64  public net.sf.basedb.info.ArrayDesignInfo getById(int itemId)
    6965    throws AxisFault
    7066  {
    71     return invokeBlocking("getById", ArrayDesignInfo.class,
     67    return invokeBlocking("getById", net.sf.basedb.info.ArrayDesignInfo.class,
    7268      session.getId(), itemId);
    7369  }
    … …  
    7975      @throws AxisFault If communication with web service fails.
    8076   */
    81   public ArrayDesignInfo[] getArrayDesigns(QueryOptions qOpt)
     77  public net.sf.basedb.info.ArrayDesignInfo[] getArrayDesigns(net.sf.basedb.info.QueryOptions qOpt)
    8278    throws AxisFault
    8379  {
    84     ArrayDesignInfo[] result = invokeBlocking("getArrayDesigns", ArrayDesignInfo[].class, session.getId(), qOpt);
     80    net.sf.basedb.info.ArrayDesignInfo[] result = invokeBlocking("getArrayDesigns", net.sf.basedb.info.ArrayDesignInfo[].class, session.getId(), qOpt);
    8581    return result;
    8682  }
    … …  
    118114      @throws AxisFault If communication with the webservice fails.
    119115   */
    120   public DataFileTypeInfo[] getDataFileTypes(int arrayDesignId, QueryOptions qOpt)
     116  public net.sf.basedb.info.DataFileTypeInfo[] getDataFileTypes(int arrayDesignId, net.sf.basedb.info.QueryOptions qOpt)
    121117    throws AxisFault
    122118  {
    … …  
    124120      (
    125121        "getDataFileTypes",
    126         DataFileTypeInfo[].class,
     122        net.sf.basedb.info.DataFileTypeInfo[].class,
    127123        session.getId(),
    128124        arrayDesignId,
    … …  
    140136      @since 3.0
    141137  */
    142   public FileSetMemberInfo[] getDataFiles(int arrayDesignId, QueryOptions qOpt)
     138  public net.sf.basedb.info.FileSetMemberInfo[] getDataFiles(int arrayDesignId, net.sf.basedb.info.QueryOptions qOpt)
    143139    throws AxisFault
    144140  {
    … …  
    146142        (
    147143          "getDataFiles",
    148           FileSetMemberInfo[].class,
     144          net.sf.basedb.info.FileSetMemberInfo[].class,
    149145          session.getId(),
    150146          arrayDesignId,

  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/BioAssaySetClient.java

    r6434 r6435  
    2424import java.io.IOException;
    2525import java.io.InputStream;
    26 
    27 import net.sf.basedb.info.DataFileTypeInfo;
    28 import net.sf.basedb.info.FileSetMemberInfo;
    29 import net.sf.basedb.info.QueryOptions;
    3026
    3127import org.apache.axis2.AxisFault;
    … …  
    8682      @since 2.12
    8783  */
    88   public DataFileTypeInfo[] getDataFileTypes(int bioAssaySetId, QueryOptions qOpt)
     84  public net.sf.basedb.info.DataFileTypeInfo[] getDataFileTypes(int bioAssaySetId, net.sf.basedb.info.QueryOptions qOpt)
    8985    throws AxisFault
    9086  {
    … …  
    9288      (
    9389        "getDataFileTypes",
    94         DataFileTypeInfo[].class,
     90        net.sf.basedb.info.DataFileTypeInfo[].class,
    9591        session.getId(),
    9692        bioAssaySetId,
    … …  
    108104      @since 3.0
    109105  */
    110   public FileSetMemberInfo[] getDataFiles(int bioAssaySetId, QueryOptions qOpt)
     106  public net.sf.basedb.info.FileSetMemberInfo[] getDataFiles(int bioAssaySetId, net.sf.basedb.info.QueryOptions qOpt)
    111107    throws AxisFault
    112108  {
    … …  
    114110        (
    115111          "getDataFiles",
    116           FileSetMemberInfo[].class,
     112          net.sf.basedb.info.FileSetMemberInfo[].class,
    117113          session.getId(),
    118114          bioAssaySetId,

  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/ExperimentClient.java

    r6434 r6435  
    2222package net.sf.basedb.ws.client;
    2323
    24 import net.sf.basedb.info.AnnotationTypeInfo;
    25 import net.sf.basedb.info.BioAssaySetInfo;
    26 import net.sf.basedb.info.ExperimentInfo;
    27 import net.sf.basedb.info.QueryOptions;
    28 import net.sf.basedb.info.RawBioAssayInfo;
    29 import net.sf.basedb.info.ReporterListInfo;
    3024
    3125import org.apache.axis2.AxisFault;
    … …  
    6054    @throws AxisFault If communication with web service fails.
    6155  */
    62   public ExperimentInfo getById(int itemId)
     56  public net.sf.basedb.info.ExperimentInfo getById(int itemId)
    6357    throws AxisFault
    6458  {
    65     return invokeBlocking("getById", ExperimentInfo.class,
     59    return invokeBlocking("getById", net.sf.basedb.info.ExperimentInfo.class,
    6660      session.getId(), itemId);
    6761  }
    … …  
    7367      @throws AxisFault If communication with web service fails.
    7468   */
    75   public ExperimentInfo[] getExperiments(QueryOptions qOpt)
     69  public net.sf.basedb.info.ExperimentInfo[] getExperiments(net.sf.basedb.info.QueryOptions qOpt)
    7670    throws AxisFault
    7771  {
    78     ExperimentInfo[] result = invokeBlocking("getExperiments", ExperimentInfo[].class, session.getId(), qOpt);
     72    net.sf.basedb.info.ExperimentInfo[] result = invokeBlocking("getExperiments", net.sf.basedb.info.ExperimentInfo[].class, session.getId(), qOpt);
    7973    return result;
    8074  }
    … …  
    8781      @throws AxisFault If communication with web services fails.
    8882   */
    89   public RawBioAssayInfo[] getRawBioAssays(int experimentId, QueryOptions qOpt)
     83  public net.sf.basedb.info.RawBioAssayInfo[] getRawBioAssays(int experimentId, net.sf.basedb.info.QueryOptions qOpt)
    9084    throws AxisFault
    9185  {
    92     RawBioAssayInfo[] result = invokeBlocking("getRawBioAssays", RawBioAssayInfo[].class, session.getId(), experimentId, qOpt);
     86    net.sf.basedb.info.RawBioAssayInfo[] result = invokeBlocking("getRawBioAssays", net.sf.basedb.info.RawBioAssayInfo[].class, session.getId(), experimentId, qOpt);
    9387    return result;
    9488  }
    … …  
    10195      @throws AxisFault If communication with web services fails.
    10296   */
    103   public BioAssaySetInfo[] getBioAssaySets(int experimentId, QueryOptions qOpt)
     97  public net.sf.basedb.info.BioAssaySetInfo[] getBioAssaySets(int experimentId, net.sf.basedb.info.QueryOptions qOpt)
    10498    throws AxisFault
    10599  {
    106     BioAssaySetInfo[] result = invokeBlocking("getBioAssaySets", BioAssaySetInfo[].class, session.getId(), experimentId, qOpt);
     100    net.sf.basedb.info.BioAssaySetInfo[] result = invokeBlocking("getBioAssaySets", net.sf.basedb.info.BioAssaySetInfo[].class, session.getId(), experimentId, qOpt);
    107101    return result;
    108102  }
    … …  
    116110      @throws AxisFault If communication with web services fails.
    117111  */
    118   public AnnotationTypeInfo[] getExperimentalFactors(int experimentId, QueryOptions qOpt)
     112  public net.sf.basedb.info.AnnotationTypeInfo[] getExperimentalFactors(int experimentId, net.sf.basedb.info.QueryOptions qOpt)
    119113    throws AxisFault
    120114  {
    121     AnnotationTypeInfo[] result = invokeBlocking("getExperimentalFactors", AnnotationTypeInfo[].class, session.getId(), experimentId, qOpt);
     115    net.sf.basedb.info.AnnotationTypeInfo[] result = invokeBlocking("getExperimentalFactors", net.sf.basedb.info.AnnotationTypeInfo[].class, session.getId(), experimentId, qOpt);
    122116    return result;
    123117  }
    … …  
    131125      @throws AxisFault If communication with web services fails.
    132126   */
    133   public ReporterListInfo[] getReporterLists(int experimentId, QueryOptions qOpt)
     127  public net.sf.basedb.info.ReporterListInfo[] getReporterLists(int experimentId, net.sf.basedb.info.QueryOptions qOpt)
    134128    throws AxisFault
    135129  {
    136     ReporterListInfo[] result = invokeBlocking("getReporterLists", ReporterListInfo[].class, session.getId(), experimentId, qOpt);
     130    net.sf.basedb.info.ReporterListInfo[] result = invokeBlocking("getReporterLists", net.sf.basedb.info.ReporterListInfo[].class, session.getId(), experimentId, qOpt);
    137131    return result;
    138132  }

  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/FileClient.java

    r6434 r6435  
    2525import java.io.InputStream;
    2626
    27 import net.sf.basedb.info.FileInfo;
    2827
    2928import org.apache.axis2.AxisFault;
    … …  
    6160    @throws AxisFault If communication with web service fails.
    6261  */
    63   public FileInfo getById(int itemId)
     62  public net.sf.basedb.info.FileInfo getById(int itemId)
    6463    throws AxisFault
    6564  {
    66     return invokeBlocking("getById", FileInfo.class,
     65    return invokeBlocking("getById", net.sf.basedb.info.FileInfo.class,
    6766      session.getId(), itemId);
    6867  }

  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/ProjectClient.java

    r6434 r6435  
    2222package net.sf.basedb.ws.client;
    2323
    24 import net.sf.basedb.info.ProjectInfo;
    25 import net.sf.basedb.info.QueryOptions;
    2624
    2725import org.apache.axis2.AxisFault;
    … …  
    5654    @throws AxisFault If communication with web service fails.
    5755  */
    58   public ProjectInfo getById(int itemId)
     56  public net.sf.basedb.info.ProjectInfo getById(int itemId)
    5957    throws AxisFault
    6058  {
    61     return invokeBlocking("getById", ProjectInfo.class,
     59    return invokeBlocking("getById", net.sf.basedb.info.ProjectInfo.class,
    6260      session.getId(), itemId);
    6361}
    … …  
    8179      @throws AxisFault If communication with web service fails.
    8280   */
    83   public ProjectInfo[] getProjects(QueryOptions qOpt)
     81  public net.sf.basedb.info.ProjectInfo[] getProjects(net.sf.basedb.info.QueryOptions qOpt)
    8482    throws AxisFault
    8583  {   
    86     ProjectInfo[] result = invokeBlocking("getProjects", ProjectInfo[].class, session.getId(), qOpt);
     84    net.sf.basedb.info.ProjectInfo[] result = invokeBlocking("getProjects", net.sf.basedb.info.ProjectInfo[].class, session.getId(), qOpt);
    8785    return result;
    8886  }

  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/RawBioAssayClient.java

    r6434 r6435  
    2222package net.sf.basedb.ws.client;
    2323
    24 import net.sf.basedb.info.AnnotationInfo;
    25 import net.sf.basedb.info.ArrayDesignInfo;
    26 import net.sf.basedb.info.DataFileTypeInfo;
    27 import net.sf.basedb.info.FileSetMemberInfo;
    28 import net.sf.basedb.info.QueryOptions;
    29 import net.sf.basedb.info.RawBioAssayInfo;
    3024
    3125import java.io.IOException;
    … …  
    6862    @throws AxisFault If communication with web service fails.
    6963  */
    70   public RawBioAssayInfo getById(int itemId)
    71     throws AxisFault
    72   {
    73     return invokeBlocking("getById", RawBioAssayInfo.class,
     64  public net.sf.basedb.info.RawBioAssayInfo getById(int itemId)
     65    throws AxisFault
     66  {
     67    return invokeBlocking("getById", net.sf.basedb.info.RawBioAssayInfo.class,
    7468      session.getId(), itemId);
    7569  }
    … …  
    8175      @throws AxisFault If communication with web service fails.
    8276   */
    83   public RawBioAssayInfo[] getRawBioAssays(QueryOptions qOpt)
    84     throws AxisFault
    85   {
    86     RawBioAssayInfo[] result = invokeBlocking("getRawBioAssays", RawBioAssayInfo[].class, session.getId(), qOpt);
     77  public net.sf.basedb.info.RawBioAssayInfo[] getRawBioAssays(net.sf.basedb.info.QueryOptions qOpt)
     78    throws AxisFault
     79  {
     80    net.sf.basedb.info.RawBioAssayInfo[] result = invokeBlocking("getRawBioAssays", net.sf.basedb.info.RawBioAssayInfo[].class, session.getId(), qOpt);
    8781    return result;
    8882  }
    … …  
    9488      @throws AxisFault If communication with the webservice fails.
    9589   */
    96   public ArrayDesignInfo getArrayDesign(int rawBioAssayId)
     90  public net.sf.basedb.info.ArrayDesignInfo getArrayDesign(int rawBioAssayId)
    9791    throws AxisFault
    9892  {
    … …  
    10094      (
    10195        "getArrayDesign",
    102         ArrayDesignInfo.class,
     96        net.sf.basedb.info.ArrayDesignInfo.class,
    10397        session.getId(),
    10498        rawBioAssayId
    … …  
    158152      @throws AxisFault If communication with webservice fails.
    159153   */
    160   public DataFileTypeInfo[] getDataFileTypes(int rawBioAssayId, QueryOptions qOpt)
     154  public net.sf.basedb.info.DataFileTypeInfo[] getDataFileTypes(int rawBioAssayId, net.sf.basedb.info.QueryOptions qOpt)
    161155    throws AxisFault
    162156  {
    … …  
    164158      (
    165159        "getDataFileTypes",
    166         DataFileTypeInfo[].class,
     160        net.sf.basedb.info.DataFileTypeInfo[].class,
    167161        session.getId(),
    168162        rawBioAssayId,
    … …  
    180174      @since 3.0
    181175  */
    182   public FileSetMemberInfo[] getDataFiles(int rawBioAssayId, QueryOptions qOpt)
     176  public net.sf.basedb.info.FileSetMemberInfo[] getDataFiles(int rawBioAssayId, net.sf.basedb.info.QueryOptions qOpt)
    183177    throws AxisFault
    184178  {
    … …  
    186180        (
    187181          "getDataFiles",
    188           FileSetMemberInfo[].class,
     182          net.sf.basedb.info.FileSetMemberInfo[].class,
    189183          session.getId(),
    190184          rawBioAssayId,
    … …  
    204198    @throws AxisFault
    205199  */
    206   public AnnotationInfo[] getAnnotationValues(int rawBioAssayId, Integer[] annotationTypes, boolean findInherited)
    207     throws AxisFault
    208   {
    209     return invokeBlocking("getAnnotations", AnnotationInfo[].class,
     200  public net.sf.basedb.info.AnnotationInfo[] getAnnotationValues(int rawBioAssayId, Integer[] annotationTypes, boolean findInherited)
     201    throws AxisFault
     202  {
     203    return invokeBlocking("getAnnotations", net.sf.basedb.info.AnnotationInfo[].class,
    210204      session.getId(), rawBioAssayId, annotationTypes, findInherited);
    211205  }

  • trunk/src/webservices/client/java/net/sf/basedb/ws/client/ReporterClient.java

    r6434 r6435  
    2121*/
    2222package net.sf.basedb.ws.client;
    23 
    24 import net.sf.basedb.info.ExtendedPropertyInfo;
    25 import net.sf.basedb.info.QueryOptions;
    2623
    2724import java.io.IOException;
    … …  
    6057      @throws AxisFault
    6158   */
    62   public ExtendedPropertyInfo[] getExtendedProperties()
     59  public net.sf.basedb.info.ExtendedPropertyInfo[] getExtendedProperties()
    6360    throws AxisFault
    6461  {
    65     ExtendedPropertyInfo[] result = invokeBlocking("getExtendedProperties", ExtendedPropertyInfo[].class, session.getId());
     62    net.sf.basedb.info.ExtendedPropertyInfo[] result = invokeBlocking("getExtendedProperties", net.sf.basedb.info.ExtendedPropertyInfo[].class, session.getId());
    6663    return result;
    6764  }
    … …  
    7673      @throws IOException If something goes wrong with the input stream
    7774   */
    78   public InputStream downloadReportersInList(int reporterListId, ExtendedPropertyInfo[] extPropInfo, QueryOptions qOpt)
     75  public InputStream downloadReportersInList(int reporterListId, net.sf.basedb.info.ExtendedPropertyInfo[] extPropInfo, net.sf.basedb.info.QueryOptions qOpt)
    7976    throws IOException
    8077  {
    … …  
    10198      @throws IOException If something goes wrong when getting the exported properties.
    10299   */
    103   public InputStream downloadReporters(ExtendedPropertyInfo[] extPropInfo, QueryOptions qOpt)
     100  public InputStream downloadReporters(net.sf.basedb.info.ExtendedPropertyInfo[] extPropInfo, net.sf.basedb.info.QueryOptions qOpt)
    104101    throws IOException
    105102  {

  • trunk/src/webservices/server/net/sf/basedb/ws/server/AnnotationTypeService.java

    r6434 r6435  
    2727import net.sf.basedb.core.ItemQuery;
    2828import net.sf.basedb.core.SessionControl;
    29 import net.sf.basedb.info.AnnotationTypeInfo;
    30 import net.sf.basedb.info.QueryOptions;
    3129
    3230
    … …  
    5452    @return The annotation type information
    5553  */
    56   public AnnotationTypeInfo getById(String ID, int itemId)
     54  public net.sf.basedb.info.AnnotationTypeInfo getById(String ID, int itemId)
    5755  {
    5856    SessionControl sc = getSessionControl(ID);
    … …  
    6159    {
    6260      AnnotationType at = AnnotationType.getById(dc, itemId);
    63       return at.toTransferable(new AnnotationTypeInfo());
     61      return at.toTransferable(new net.sf.basedb.info.AnnotationTypeInfo());
    6462    }
    6563    finally
    … …  
    8078      @return Information objects in an array for each found annotation type.
    8179  */
    82   public AnnotationTypeInfo[] getAnnotationTypes(String ID, String itemType, QueryOptions qOpt)
     80  public net.sf.basedb.info.AnnotationTypeInfo[] getAnnotationTypes(String ID, String itemType, net.sf.basedb.info.QueryOptions qOpt)
    8381  {
    8482    SessionControl sc = getSessionControl(ID);
    … …  
    8987      ItemQuery<AnnotationType> query = AnnotationType.getQuery(item);
    9088      query = util.getConfiguredItemQuery(query, qOpt);
    91       return util.listToInfo(query.list(dc), AnnotationTypeInfo.class);
     89      return util.listToInfo(query.list(dc), net.sf.basedb.info.AnnotationTypeInfo.class);
    9290    }
    9391    finally

  • trunk/src/webservices/server/net/sf/basedb/ws/server/ArrayDesignService.java

    r6434 r6435  
    3030import net.sf.basedb.core.ItemQuery;
    3131import net.sf.basedb.core.SessionControl;
    32 import net.sf.basedb.info.AnnotationInfo;
    33 import net.sf.basedb.info.ArrayDesignInfo;
    34 import net.sf.basedb.info.DataFileTypeInfo;
    35 import net.sf.basedb.info.FileSetMemberInfo;
    36 import net.sf.basedb.info.QueryOptions;
    3732
    3833import org.apache.axiom.om.OMElement;
    … …  
    6358    @return The array design information
    6459  */
    65   public ArrayDesignInfo getById(String ID, int itemId)
     60  public net.sf.basedb.info.ArrayDesignInfo getById(String ID, int itemId)
    6661  {
    6762    SessionControl sc = getSessionControl(ID);
    … …  
    7065    {
    7166      ArrayDesign ad = ArrayDesign.getById(dc, itemId);
    72       return ad.toTransferable(new ArrayDesignInfo());
     67      return ad.toTransferable(new net.sf.basedb.info.ArrayDesignInfo());
    7368    }
    7469    finally
    … …  
    8681      @return An ArrayDesignInfo array.
    8782   */
    88   public ArrayDesignInfo[] getArrayDesigns(String ID, QueryOptions qOpt)
     83  public net.sf.basedb.info.ArrayDesignInfo[] getArrayDesigns(String ID, net.sf.basedb.info.QueryOptions qOpt)
    8984  {
    9085    SessionControl sc = getSessionControl(ID);
    … …  
    9489      ItemQuery<ArrayDesign> query= ArrayDesign.getQuery();   
    9590      query = util.getConfiguredItemQuery(query, qOpt);
    96       return util.listToInfo(query.list(dc), ArrayDesignInfo.class);
     91      return util.listToInfo(query.list(dc), net.sf.basedb.info.ArrayDesignInfo.class);
    9792    }
    9893    finally
    … …  
    173168      @return An array with DataFileTypeInfo:s.
    174169   */
    175   public DataFileTypeInfo[] getDataFileTypes(String ID, int arrayDesignId, QueryOptions qOpt)
     170  public net.sf.basedb.info.DataFileTypeInfo[] getDataFileTypes(String ID, int arrayDesignId, net.sf.basedb.info.QueryOptions qOpt)
    176171  {
    177172    SessionControl sc = getSessionControl(ID);
    … …  
    186181        ItemQuery<DataFileType> query = fileSet.getMemberTypes();       
    187182        query = util.getConfiguredItemQuery(query, qOpt);
    188         return util.listToInfo(query.list(dc), DataFileTypeInfo.class);
     183        return util.listToInfo(query.list(dc), net.sf.basedb.info.DataFileTypeInfo.class);
    189184      }
    190185    }
    … …  
    193188      if (dc != null) dc.close();
    194189    }
    195     return new DataFileTypeInfo[0];
     190    return new net.sf.basedb.info.DataFileTypeInfo[0];
    196191  }
    197192 
    … …  
    205200      @since 3.0
    206201  */
    207   public FileSetMemberInfo[] getDataFiles(String ID, int arrayDesignId, QueryOptions qOpt)
     202  public net.sf.basedb.info.FileSetMemberInfo[] getDataFiles(String ID, int arrayDesignId, net.sf.basedb.info.QueryOptions qOpt)
    208203  {
    209204    SessionControl sc = getSessionControl(ID);
    … …  
    231226      corresponds to the annotation type with the same index in the annotationTypes array
    232227  */
    233   public AnnotationInfo[] getAnnotations(String ID, int arrayDesignId, Integer[] annotationTypes, boolean findInherited)
     228  public net.sf.basedb.info.AnnotationInfo[] getAnnotations(String ID, int arrayDesignId, Integer[] annotationTypes, boolean findInherited)
    234229  {
    235230    SessionControl sc = getSessionControl(ID);

  • trunk/src/webservices/server/net/sf/basedb/ws/server/BioAssaySetService.java

    r6434 r6435  
    2929import net.sf.basedb.core.ItemQuery;
    3030import net.sf.basedb.core.SessionControl;
    31 import net.sf.basedb.info.AnnotationInfo;
    32 import net.sf.basedb.info.DataFileTypeInfo;
    33 import net.sf.basedb.info.FileSetMemberInfo;
    34 import net.sf.basedb.info.QueryOptions;
    3531
    3632import org.apache.axiom.om.OMElement;
    … …  
    127123      @since 2.12
    128124  */
    129   public DataFileTypeInfo[] getDataFileTypes(String ID, int bioAssaySetId, QueryOptions qOpt)
     125  public net.sf.basedb.info.DataFileTypeInfo[] getDataFileTypes(String ID, int bioAssaySetId, net.sf.basedb.info.QueryOptions qOpt)
    130126  {
    131127    SessionControl sc = getSessionControl(ID);
    … …  
    138134        ItemQuery<DataFileType> query = bas.getFileSet().getMemberTypes();
    139135        query = util.getConfiguredItemQuery(query, qOpt);
    140         return util.listToInfo(query.list(dc), DataFileTypeInfo.class);
     136        return util.listToInfo(query.list(dc), net.sf.basedb.info.DataFileTypeInfo.class);
    141137      }
    142138    }
    … …  
    145141      if (dc != null) dc.close();
    146142    }
    147     return new DataFileTypeInfo[0];
     143    return new net.sf.basedb.info.DataFileTypeInfo[0];
    148144  }
    149145
    … …  
    157153      @since 3.0
    158154  */
    159   public FileSetMemberInfo[] getDataFiles(String ID, int bioAssaySetId, QueryOptions qOpt)
     155  public net.sf.basedb.info.FileSetMemberInfo[] getDataFiles(String ID, int bioAssaySetId, net.sf.basedb.info.QueryOptions qOpt)
    160156  {
    161157    SessionControl sc = getSessionControl(ID);
    … …  
    183179      corresponds to the annotation type with the same index in the annotationTypes array
    184180  */
    185   public AnnotationInfo[] getAnnotations(String ID, int bioAssaySetId, Integer[] annotationTypes, boolean findInherited)
     181  public net.sf.basedb.info.AnnotationInfo[] getAnnotations(String ID, int bioAssaySetId, Integer[] annotationTypes, boolean findInherited)
    186182  {
    187183    SessionControl sc = getSessionControl(ID);

  • trunk/src/webservices/server/net/sf/basedb/ws/server/ExperimentService.java

    r6434 r6435  
    3232import net.sf.basedb.core.query.Hql;
    3333import net.sf.basedb.core.query.Restrictions;
    34 import net.sf.basedb.info.AnnotationTypeInfo;
    35 import net.sf.basedb.info.BioAssaySetInfo;
    36 import net.sf.basedb.info.ExperimentInfo;
    37 import net.sf.basedb.info.QueryOptions;
    38 import net.sf.basedb.info.RawBioAssayInfo;
    39 import net.sf.basedb.info.ReporterListInfo;
    4034
    4135/**
    … …  
    6256    @return The experiment information
    6357  */
    64   public ExperimentInfo getById(String ID, int itemId)
     58  public net.sf.basedb.info.ExperimentInfo getById(String ID, int itemId)
    6559  {
    6660    SessionControl sc = getSessionControl(ID);
    … …  
    6963    {
    7064      Experiment e = Experiment.getById(dc, itemId);
    71       return e.toTransferable(new ExperimentInfo());
     65      return e.toTransferable(new net.sf.basedb.info.ExperimentInfo());
    7266    }
    7367    finally
    … …  
    8579      @return An ExperimentInfo array.
    8680   */
    87   public ExperimentInfo[] getExperiments(String ID, QueryOptions qOpt)
     81  public net.sf.basedb.info.ExperimentInfo[] getExperiments(String ID, net.sf.basedb.info.QueryOptions qOpt)
    8882  {
    8983    SessionControl sc = getSessionControl(ID);
    … …  
    9387      ItemQuery<Experiment> query= Experiment.getQuery();   
    9488      query = util.getConfiguredItemQuery(query, qOpt);
    95       return util.listToInfo(query.list(dc), ExperimentInfo.class);
     89      return util.listToInfo(query.list(dc), net.sf.basedb.info.ExperimentInfo.class);
    9690    }
    9791    finally
    … …  
    109103      @return Array of ItemInfo:s, one for each bioassay set that where found by the query.
    110104   */
    111   public BioAssaySetInfo[] getBioAssaySets(String ID, int experimentId, QueryOptions qOpt)
     105  public net.sf.basedb.info.BioAssaySetInfo[] getBioAssaySets(String ID, int experimentId, net.sf.basedb.info.QueryOptions qOpt)
    112106  {
    113107    SessionControl sc = getSessionControl(ID);
    … …  
    118112      ItemQuery<BioAssaySet> query = experiment.getBioAssaySets();
    119113      query = util.getConfiguredItemQuery(query, qOpt);
    120       return util.listToInfo(query.list(dc), BioAssaySetInfo.class);
     114      return util.listToInfo(query.list(dc), net.sf.basedb.info.BioAssaySetInfo.class);
    121115    }
    122116    finally
    … …  
    134128      @return Array with {@link net.sf.basedb.info.RawBioAssayInfo}s
    135129   */
    136   public RawBioAssayInfo[] getRawBioAssays(String ID, int experimentId, QueryOptions qOpt)
     130  public net.sf.basedb.info.RawBioAssayInfo[] getRawBioAssays(String ID, int experimentId, net.sf.basedb.info.QueryOptions qOpt)
    137131  {
    138132    SessionControl sc = getSessionControl(ID);
    … …  
    143137      ItemQuery<RawBioAssay> query = experiment.getRawBioAssays();     
    144138      query = util.getConfiguredItemQuery(query, qOpt);
    145       return util.listToInfo(query.list(dc), RawBioAssayInfo.class);
     139      return util.listToInfo(query.list(dc), net.sf.basedb.info.RawBioAssayInfo.class);
    146140    }
    147141    finally
    … …  
    159153      @return ReporterListInfo array.
    160154   */
    161   public ReporterListInfo[] getReporterLists(String ID, int experimentId, QueryOptions qOpt)
     155  public net.sf.basedb.info.ReporterListInfo[] getReporterLists(String ID, int experimentId, net.sf.basedb.info.QueryOptions qOpt)
    162156  {
    163157    SessionControl sc = getSessionControl(ID);
    … …  
    168162      ItemQuery<ReporterList> query = ReporterList.getQuery(); 
    169163      query.restrictPermanent(Restrictions.eq(Hql.property("experiment"), Hql.entity(experiment)));
    170       return util.listToInfo(query.list(dc), ReporterListInfo.class);
     164      return util.listToInfo(query.list(dc), net.sf.basedb.info.ReporterListInfo.class);
    171165    }
    172166    finally
    … …  
    184178      @return Array with {@link net.sf.basedb.info.AnnotationTypeInfo}:s
    185179  */
    186   public AnnotationTypeInfo[] getExperimentalFactors(String ID, int experimentId, QueryOptions qOpt)
     180  public net.sf.basedb.info.AnnotationTypeInfo[] getExperimentalFactors(String ID, int experimentId, net.sf.basedb.info.QueryOptions qOpt)
    187181  {
    188182    SessionControl sc = getSessionControl(ID);
    … …  
    193187      ItemQuery<AnnotationType> query = experiment.getExperimentalFactors();     
    194188      query = util.getConfiguredItemQuery(query, qOpt);
    195       return util.listToInfo(query.list(dc), AnnotationTypeInfo.class);
     189      return util.listToInfo(query.list(dc), net.sf.basedb.info.AnnotationTypeInfo.class);
    196190    }
    197191    finally

  • trunk/src/webservices/server/net/sf/basedb/ws/server/FileService.java

    r6434 r6435  
    2727import net.sf.basedb.core.File;
    2828import net.sf.basedb.core.SessionControl;
    29 import net.sf.basedb.info.FileInfo;
    3029
    3130
    … …  
    5352    @return The file information
    5453  */
    55   public FileInfo getById(String ID, int itemId)
     54  public net.sf.basedb.info.FileInfo getById(String ID, int itemId)
    5655  {
    5756    SessionControl sc = getSessionControl(ID);
    … …  
    6059    {
    6160      File f = File.getById(dc, itemId);
    62       return f.toTransferable(new FileInfo());
     61      return f.toTransferable(new net.sf.basedb.info.FileInfo());
    6362    }
    6463    finally

  • trunk/src/webservices/server/net/sf/basedb/ws/server/ProjectService.java

    r6434 r6435  
    2626import net.sf.basedb.core.Project;
    2727import net.sf.basedb.core.SessionControl;
    28 import net.sf.basedb.info.ProjectInfo;
    29 import net.sf.basedb.info.QueryOptions;
    3028
    3129
    … …  
    5351    @return The project information
    5452  */
    55   public ProjectInfo getById(String ID, int itemId)
     53  public net.sf.basedb.info.ProjectInfo getById(String ID, int itemId)
    5654  {
    5755    SessionControl sc = getSessionControl(ID);
    … …  
    6058    {
    6159      Project p = Project.getById(dc, itemId);
    62       return p.toTransferable(new ProjectInfo());
     60      return p.toTransferable(new net.sf.basedb.info.ProjectInfo());
    6361    }
    6462    finally
    … …  
    10199      @return Information objects in an array for each found project.
    102100   */
    103   public ProjectInfo[] getProjects(String ID, QueryOptions qOpt)
     101  public net.sf.basedb.info.ProjectInfo[] getProjects(String ID, net.sf.basedb.info.QueryOptions qOpt)
    104102  {
    105103    SessionControl sc = getSessionControl(ID);
    … …  
    109107      ItemQuery<Project> query = Project.getQuery();
    110108      query = util.getConfiguredItemQuery(query, qOpt);
    111       return util.listToInfo(query.list(dc), ProjectInfo.class);
     109      return util.listToInfo(query.list(dc), net.sf.basedb.info.ProjectInfo.class);
    112110    }
    113111    finally

  • trunk/src/webservices/server/net/sf/basedb/ws/server/RawBioAssayService.java

    r6434 r6435  
    3030import net.sf.basedb.core.RawBioAssay;
    3131import net.sf.basedb.core.SessionControl;
    32 import net.sf.basedb.info.AnnotationInfo;
    33 import net.sf.basedb.info.ArrayDesignInfo;
    34 import net.sf.basedb.info.DataFileTypeInfo;
    35 import net.sf.basedb.info.FileSetMemberInfo;
    36 import net.sf.basedb.info.QueryOptions;
    37 import net.sf.basedb.info.RawBioAssayInfo;
    3832
    3933import org.apache.axiom.om.OMElement;
    … …  
    6256    @return The raw bioassay information
    6357  */
    64   public RawBioAssayInfo getById(String ID, int itemId)
     58  public net.sf.basedb.info.RawBioAssayInfo getById(String ID, int itemId)
    6559  {
    6660    SessionControl sc = getSessionControl(ID);
    … …  
    6963    {
    7064      RawBioAssay rba = RawBioAssay.getById(dc, itemId);
    71       return rba.toTransferable(new RawBioAssayInfo());
     65      return rba.toTransferable(new net.sf.basedb.info.RawBioAssayInfo());
    7266    }
    7367    finally
    … …  
    8478      @return An RawBioAssayInfo array.
    8579   */
    86   public RawBioAssayInfo[] getRawBioAssays(String ID, QueryOptions qOpt)
     80  public net.sf.basedb.info.RawBioAssayInfo[] getRawBioAssays(String ID, net.sf.basedb.info.QueryOptions qOpt)
    8781  {
    8882    SessionControl sc = getSessionControl(ID);
    … …  
    9286      ItemQuery<RawBioAssay> query= RawBioAssay.getQuery();   
    9387      query = util.getConfiguredItemQuery(query, qOpt);
    94       return util.listToInfo(query.list(dc), RawBioAssayInfo.class);
     88      return util.listToInfo(query.list(dc), net.sf.basedb.info.RawBioAssayInfo.class);
    9589    }
    9690    finally
    … …  
    106100      @return ArrayDesignInfo object containing information about the used arraydesign.
    107101   */
    108   public ArrayDesignInfo getArrayDesign(String ID, int rawBioAssayId)
    109   {
    110     SessionControl sc = getSessionControl(ID);
    111     DbControl dc = sc.newDbControl();
    112     ArrayDesignInfo info = null;
     102  public net.sf.basedb.info.ArrayDesignInfo getArrayDesign(String ID, int rawBioAssayId)
     103  {
     104    SessionControl sc = getSessionControl(ID);
     105    DbControl dc = sc.newDbControl();
     106    net.sf.basedb.info.ArrayDesignInfo info = null;
    113107    try
    114108    {
    115109      RawBioAssay rawBioAssay = RawBioAssay.getById(dc, rawBioAssayId);
    116110      ArrayDesign arrayDesign = rawBioAssay.getArrayDesign();
    117       if (arrayDesign != null) info = arrayDesign.toTransferable(new ArrayDesignInfo());
     111      if (arrayDesign != null) info = arrayDesign.toTransferable(new net.sf.basedb.info.ArrayDesignInfo());
    118112    }
    119113    finally
    … …  
    198192      @return An array with DataFileTypeInfo:s.
    199193   */
    200   public DataFileTypeInfo[] getDataFileTypes(String ID, int rawBioAssayId, QueryOptions qOpt)
     194  public net.sf.basedb.info.DataFileTypeInfo[] getDataFileTypes(String ID, int rawBioAssayId, net.sf.basedb.info.QueryOptions qOpt)
    201195  {
    202196    SessionControl sc = getSessionControl(ID);
    … …  
    209203        ItemQuery<DataFileType> query = rawBioAssay.getFileSet().getMemberTypes();
    210204        query = util.getConfiguredItemQuery(query, qOpt);
    211         return util.listToInfo(query.list(dc), DataFileTypeInfo.class);
     205        return util.listToInfo(query.list(dc), net.sf.basedb.info.DataFileTypeInfo.class);
    212206      }
    213207    }
    … …  
    216210      if (dc != null) dc.close();
    217211    }
    218     return new DataFileTypeInfo[0];
     212    return new net.sf.basedb.info.DataFileTypeInfo[0];
    219213  }
    220214 
    … …  
    228222      @since 3.0
    229223  */
    230   public FileSetMemberInfo[] getDataFiles(String ID, int rawBioAssayId, QueryOptions qOpt)
     224  public net.sf.basedb.info.FileSetMemberInfo[] getDataFiles(String ID, int rawBioAssayId, net.sf.basedb.info.QueryOptions qOpt)
    231225  {
    232226    SessionControl sc = getSessionControl(ID);
    … …  
    254248      corresponds to the annotation type with the same index in the annotationTypes array
    255249  */
    256   public AnnotationInfo[] getAnnotations(String ID, int rawBioAssayId, Integer[] annotationTypes, boolean findInherited)
     250  public net.sf.basedb.info.AnnotationInfo[] getAnnotations(String ID, int rawBioAssayId, Integer[] annotationTypes, boolean findInherited)
    257251  {
    258252    SessionControl sc = getSessionControl(ID);

  • trunk/src/webservices/server/net/sf/basedb/ws/server/ReporterService.java

    r6434 r6435  
    4141import net.sf.basedb.core.query.Hql;
    4242import net.sf.basedb.core.query.Query;
    43 import net.sf.basedb.info.ExtendedPropertyInfo;
    44 import net.sf.basedb.info.QueryOptions;
    4543import net.sf.basedb.util.formatter.Formatter;
    4644import net.sf.basedb.util.formatter.MultiFormatter;
    … …  
    8078      @return an ExtendedPropertyInfo array.
    8179   */
    82   public ExtendedPropertyInfo[] getExtendedProperties()
     80  public net.sf.basedb.info.ExtendedPropertyInfo[] getExtendedProperties()
    8381  {
    8482    List<ExtendedProperty> properties = ExtendedProperties.getProperties("ReporterData");
    8583    if (properties != null)
    8684    {
    87       return util.listToInfo(properties, ExtendedPropertyInfo.class);
     85      return util.listToInfo(properties, net.sf.basedb.info.ExtendedPropertyInfo.class);
    8886    }
    8987    else
    9088    {
    91       return new ExtendedPropertyInfo[0];
     89      return new net.sf.basedb.info.ExtendedPropertyInfo[0];
    9290    }
    9391  }
    … …  
    102100      @throws Exception If something goes wrong with the export.
    103101   */
    104   public OMElement downloadReportersInList(String ID, int reporterListId, ExtendedPropertyInfo[] extPropInfos, QueryOptions qOpt)
     102  public OMElement downloadReportersInList(String ID, int reporterListId, net.sf.basedb.info.ExtendedPropertyInfo[] extPropInfos, net.sf.basedb.info.QueryOptions qOpt)
    105103    throws Exception
    106104  {   
    … …  
    125123    exportedProperties.add(ExportedProperty.createExportedProperty("reporter.reporterType.name", "Reporter type", metadata, formatter));
    126124    exportedProperties.add(ExportedProperty.createExportedProperty("score", "Score", metadata, formatter));
    127     for (ExtendedPropertyInfo ep : extPropInfos)
     125    for (net.sf.basedb.info.ExtendedPropertyInfo ep : extPropInfos)
    128126    {
    129127      exportedProperties.add(ExportedProperty.createExportedProperty("reporter." + ep.getName(), ep.getTitle(), metadata, formatter));
    … …  
    167165      @throws Exception If anything goes wrong with the export.
    168166   */
    169   public OMElement downloadReporters(String ID, ExtendedPropertyInfo[] extPropInfos, QueryOptions qOpt)
     167  public OMElement downloadReporters(String ID, net.sf.basedb.info.ExtendedPropertyInfo[] extPropInfos, net.sf.basedb.info.QueryOptions qOpt)
    170168    throws Exception
    171169  {
    … …  
    189187    exportedProperties.add(ExportedProperty.createExportedProperty("externalId", "External ID", metadata, formatter));
    190188    exportedProperties.add(ExportedProperty.createExportedProperty("reporterType.name", "Reporter type", metadata, formatter));
    191     for (ExtendedPropertyInfo ep : extPropInfos)
     189    for (net.sf.basedb.info.ExtendedPropertyInfo ep : extPropInfos)
    192190    {
    193191      exportedProperties.add(ExportedProperty.createExportedProperty(ep.getName(), ep.getTitle(), metadata, formatter));

  • trunk/src/webservices/server/net/sf/basedb/ws/server/SessionService.java

    r6434 r6435  
    2525import net.sf.basedb.core.SessionControl;
    2626import net.sf.basedb.core.authentication.LoginRequest;
    27 import net.sf.basedb.info.VersionInfo;
    2827
    2928/**
    … …  
    113112      @return A {@link VersionInfo} object
    114113   */
    115   public VersionInfo getVersion()
     114  public net.sf.basedb.info.VersionInfo getVersion()
    116115  {
    117     VersionInfo info = new VersionInfo();
     116    net.sf.basedb.info.VersionInfo info = new net.sf.basedb.info.VersionInfo();
    118117    info.setMajor(Application.getMajorVersion());
    119118    info.setMinor(Application.getMinorVersion());
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