Changeset 4305


Ignore:
Timestamp:
May 21, 2008, 1:11:20 PM (14 years ago)
Author:
Nicklas Nordborg
Message:

References #1015: Add reporter list from tables that list reporters/reporter info

It is now possible to create reporter lists from features, wells and raw data, eg. all DataQuery?-based item types. Creating the lists using queries from the dynamic database needs a different solution.

Location:
trunk
Files:
15 edited

Legend:

Unmodified
Added
Removed

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

    r4302 r4305  
    7272
    7373  /**
    74     The item type returned by the query.
    75   */
    76   private final Item itemType;
     74    The item type returned by the query, eg.
     75    SELECT [returnType] FROM ...
     76  */
     77  private final Item returnType;
     78 
     79  /**
     80    The root item type we start with in the query. eq.
     81    SELECT ... FROM [rootTypeTable]
     82    @since 2.8
     83  */
     84  private final Item rootType;
    7785 
    7886  /**
    … …  
    134142    Create a new query returning items of the specified item type
    135143    using the default optional runtime filter.
    136     @param itemType The type of items that are returned
     144    @param returnType The type of items that are returned
     145    @param entityName The name of the type of items as known to
     146      Hibernate, or null to use the class of the return type
    137147    @param stateless TRUE if the stateless Hibernate session should be used, FALSE
    138148      if the regular Hibernate session should be used
    139149  */
    140   AbstractEntityQuery(Item itemType, String entityName, boolean stateless)
    141   {
    142     this(itemType, entityName, stateless, QueryRuntimeFilterFactory.getOptionalFilter(itemType));
     150  AbstractEntityQuery(Item returnType, String entityName, boolean stateless)
     151  {
     152    this(returnType, returnType, entityName, null, stateless,
     153        QueryRuntimeFilterFactory.getOptionalFilter(returnType));
    143154  }
    144155 
    … …  
    146157    Create a new query returning items of the specified type with a non-default
    147158    optional runtime filter.
    148     @param itemType The type of items that are returned
     159    @param returnType The type of items that are returned
     160    @param entityName The name of the type of items as known to
     161      Hibernate, or null to use the class of the return type
    149162    @param stateless TRUE if the stateless Hibernate session should be used, FALSE
    150163      if the regular Hibernate session should be used
    … …  
    152165      or null to not use any optional filter
    153166  */
    154   AbstractEntityQuery(Item itemType, String entityName, boolean stateless, QueryRuntimeFilter optionalFilter)
    155   {
    156     super(entityName == null ? itemType.getDataClass().getName() : entityName);
    157     this.itemType = itemType;
     167  AbstractEntityQuery(Item returnType, String entityName, boolean stateless, QueryRuntimeFilter optionalFilter)
     168  {
     169    this(returnType, returnType, entityName, null, stateless, optionalFilter);
     170  }
     171
     172  /**
     173    Create a new query that may have different return type and root item type.
     174
     175    @see DataQuery#DataQuery(Class, Item, String, String)
     176    @since 2.8
     177  */
     178  AbstractEntityQuery(Item returnType, Item rootType, String rootName, String select,
     179      boolean stateless, QueryRuntimeFilter optionalFilter)
     180  {
     181    super(rootName == null ? rootType.getDataClass().getName() : rootName);
     182    super.selectPermanent(Selects.expression(Hql.property(rootType.getAlias(), select), null, true));
     183    this.returnType = returnType;
     184    this.rootType = rootType;
    158185    this.stateless = stateless;
    159     this.requiredFilter = QueryRuntimeFilterFactory.getRequiredFilter(itemType);
     186    this.requiredFilter = QueryRuntimeFilterFactory.getRequiredFilter(rootType);
    160187    this.optionalFilter = optionalFilter;
    161     super.selectPermanent(Selects.expression(Hql.alias(itemType.getAlias()), null, true));
    162188    this.includes = EnumSet.of(Include.NOT_REMOVED, Include.MINE, Include.IN_PROJECT,
    163       Include.ANNOTATED, Include.NOT_ANNOTATED);
     189        Include.ANNOTATED, Include.NOT_ANNOTATED);
    164190    this.permission = Permission.READ;
    165191    setAutoJoinType(JoinType.LEFT);
    166192  }
    167 
    168193 
    169194  /*
    … …  
    231256 
    232257  /**
    233     The alias of the item that is returned by this query.
     258    The alias of the item that is the root of this query.
    234259    @see Item#getAlias()
    235260  */
    236261  public String getRootAlias()
    237262  {
    238     return itemType.getAlias();
     263    return rootType.getAlias();
    239264  }
    240265 
    … …  
    299324  public Item getItemType()
    300325  {
    301     return itemType;
     326    return returnType;
     327  }
     328  /**
     329    @since 2.8
     330  */
     331  public Item getRootType()
     332  {
     333    return rootType;
    302334  }
    303335  public void include(Include... includes)

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

    r4257 r4305  
    2929import net.sf.basedb.core.data.ArrayDesignPlateData;
    3030import net.sf.basedb.core.data.FeatureData;
     31import net.sf.basedb.core.data.ReporterData;
    3132import net.sf.basedb.core.query.Hql;
    3233import net.sf.basedb.core.query.Restrictions;
    … …  
    777778
    778779  /**
     780    Get a query that returns the reporters on this array design. The query
     781    is rooted at the features, which means that:
     782    <ul>
     783    <li>All filters, sorting, etc. that works for {@link #getFeatures()} can be
     784      used without modifications on this query.
     785    <li>The same reporter may be returned multiple times if it is present on several
     786      features.
     787    <li>'Null' values may be returned if there are features without a reporter
     788    </ul>
     789   
     790    @return A {@link DataQuery} object
     791    @since 2.8
     792  */
     793  public DataQuery<ReporterData> getReporters()
     794  {
     795    DataQuery<ReporterData> query =
     796      new DataQuery<ReporterData>(ReporterData.class, Item.FEATURE, null, "reporter");
     797    query.restrictPermanent(
     798        Restrictions.eq(
     799          Hql.property("arrayDesignBlock.arrayDesign"),
     800          Hql.entity(this)
     801        )
     802      );
     803    return query;
     804  }
     805 
     806  /**
    779807    Get a feature when you know the id.
    780808    @param id The id of the feature

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

    r4243 r4305  
    6262 
    6363  /**
     64    Create a query that may have different return type and root entity.
     65    For example, to return reporters from a query rooted at features:
     66    <code>new DataQuery(ReporterData.class, Item.FEATURE, null, "reporter")</code>.
     67    This will be translated to something like (in HQL):
     68    <code>SELECT ftr.reporter FROM FeatureData ftr ...</code>
     69
     70    @param dataClass The class of the data objects that are returned
     71    @param rootType The root item type of the query
     72    @param rootName The root enitity name, or null to use
     73      the class name of the root type
     74    @param select The HQL property that we should select on the root
     75      type to get to the return type
     76    @since 2.8
     77  */
     78  DataQuery(Class<I> dataClass, Item rootType, String rootName, String select)
     79  {
     80    super(Item.fromDataClass(dataClass), rootType, rootName, select, true,
     81      QueryRuntimeFilterFactory.getOptionalFilter(rootType));
     82    this.dataClass = dataClass;
     83  }
     84 
     85  /**
    6486    Create a new query for the specified item, using a non-default optional
    6587    runtime filter.

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

    r4040 r4305  
    2828import net.sf.basedb.core.data.PlateEventData;
    2929import net.sf.basedb.core.data.PlateCoordinate;
     30import net.sf.basedb.core.data.ReporterData;
    3031import net.sf.basedb.core.data.WellData;
    3132import net.sf.basedb.core.query.Restrictions;
    … …  
    483484  }
    484485 
     486  /**
     487    Get a query that returns the reporters on this plate. The query
     488    is rooted at the wells, which means that:
     489    <ul>
     490    <li>All filters, sorting, etc. that works for {@link #getWells()} can be
     491      used without modifications on this query.
     492    <li>The same reporter may be returned multiple times if it is present on several
     493      wells.
     494    <li>'Null' values may be returned if there are wells without a reporter
     495    </ul>
     496   
     497    @return A {@link DataQuery} object
     498    @since 2.8
     499  */
     500  public DataQuery<ReporterData> getReporters()
     501  {
     502    DataQuery<ReporterData> query =
     503      new DataQuery<ReporterData>(ReporterData.class, Item.WELL, null, "reporter");
     504    query.restrictPermanent(
     505        Restrictions.eq(
     506          Hql.property("plate"),
     507          Hql.entity(this)
     508        )
     509      );
     510    return query;
     511  }
     512 
    485513}

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

    r4284 r4305  
    11371137    }
    11381138    DataQuery<RawData> query = new DataQuery<RawData>(RawData.class, rdt.getEntityName());
     1139    query.restrictPermanent(
     1140      Restrictions.eq(
     1141        Hql.property("rawBioAssay"),
     1142        Hql.entity(this)
     1143      )
     1144    );
     1145    return query;
     1146  }
     1147 
     1148  /**
     1149    Get a query that returns the reporters on this raw bioassay.
     1150    The query is rooted at the raw data, which means that:
     1151    <ul>
     1152    <li>All filters, sorting, etc. that works for {@link #getRawData()} can be
     1153      used without modifications on this query.
     1154    <li>The same reporter may be returned multiple times if it is present on multiple
     1155      spots.
     1156    <li>'Null' values may be returned if there are spots without a reporter
     1157    </ul>
     1158   
     1159    @return A {@link DataQuery} object
     1160    @since 2.8 
     1161  */
     1162  public DataQuery<ReporterData> getReporters()
     1163  {
     1164    RawDataType rdt = getRawDataType();
     1165    if (!rdt.isStoredInDb())
     1166    {
     1167      throw new BaseException("Raw data for raw data type '" + rdt + "' is not stored in the database.");
     1168    }
     1169    DataQuery<ReporterData> query =
     1170      new DataQuery<ReporterData>(ReporterData.class, Item.RAWDATA, rdt.getEntityName(), "reporter");
    11391171    query.restrictPermanent(
    11401172      Restrictions.eq(

  • trunk/src/core/net/sf/basedb/core/query/EntityQuery.java

    r3679 r4305  
    4949  */
    5050  public Item getItemType();
     51 
     52  /**
     53    The type of items that is the root of the query. In most cases,
     54    this is the same as the {@link #getItemType()}, but not
     55    always.
     56    @since 2.8
     57  */
     58  public Item getRootType();
    5159 
    5260  /**

  • trunk/www/lims/arraydesigns/features/index.jsp

    r4093 r4305  
    3737  import="net.sf.basedb.core.ArrayDesign"
    3838  import="net.sf.basedb.core.data.FeatureData"
     39  import="net.sf.basedb.core.data.ReporterData"
    3940  import="net.sf.basedb.clients.web.Base"
    4041  import="net.sf.basedb.clients.web.WebException"
    … …  
    103104    redirect = "../../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+features+of+array+design";
    104105  }
     106  else if ("CreateReporterList".equals(cmd))
     107  {
     108    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
     109    dc = sc.newDbControl();   
     110    final ArrayDesign arrayDesign = ArrayDesign.getById(dc, arrayDesignId);
     111    final DataQuery<ReporterData> query = arrayDesign.getReporters();
     112    cc.configureQuery(query, true);
     113    cc.setQuery(query);
     114    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
     115      "&cmd=NewItem&addReporters=1&formId=features&fromContext=FEATURE" +
     116      "&name=" + HTML.urlEncode(arrayDesign.getName());
     117  }
    105118  else
    106119  {

  • trunk/www/lims/arraydesigns/features/list_features.jsp

    r4302 r4305  
    156156      }
    157157    }
     158    function newReporterList()
     159    {
     160      Table.submitToPopup(formId, 'CreateReporterList', 540, 400);
     161    }
    158162    </script>
    159163  </base:head>
    … …  
    465469          title="Columns&hellip;"
    466470          tooltip="Show, hide and re-order columns"
     471        />
     472        <tbl:button
     473          image="add.png"
     474          onclick="newReporterList()"
     475          title="New reporter list&hellip;"
     476          tooltip="Create a new reporter list from matching features"
     477          visible="<%=sc.hasPermission(Permission.CREATE, Item.REPORTERLIST)%>"
    467478        />
    468479        <tbl:button

  • trunk/www/lims/plates/wells/index.jsp

    r3679 r4305  
    3333  import="net.sf.basedb.core.Well"
    3434  import="net.sf.basedb.core.ItemQuery"
     35  import="net.sf.basedb.core.DataQuery"
    3536  import="net.sf.basedb.core.Permission"
    3637  import="net.sf.basedb.core.PermissionDeniedException"
     38  import="net.sf.basedb.core.data.ReporterData"
    3739  import="net.sf.basedb.util.RemovableUtil"
    3840  import="net.sf.basedb.clients.web.Base"
    … …  
    174176    redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=OTHER&title=Run+plugin";
    175177  }
     178  else if ("CreateReporterList".equals(cmd))
     179  {
     180    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
     181    dc = sc.newDbControl();   
     182    final Plate plate = Plate.getById(dc, plateId);
     183    final DataQuery<ReporterData> query = plate.getReporters();
     184    cc.configureQuery(query, true);
     185    cc.setQuery(query);
     186    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
     187      "&cmd=NewItem&addReporters=1&formId=wells&fromContext=WELL"+
     188      "&name=" + HTML.urlEncode(plate.getName());
     189  }
    176190  else
    177191  {

  • trunk/www/lims/plates/wells/list_wells.jsp

    r4302 r4305  
    162162      }
    163163    }
     164    function newReporterList()
     165    {
     166      Table.submitToPopup(formId, 'CreateReporterList', 540, 400);
     167    }
    164168    </script>
    165169  </base:head>
    … …  
    376380          title="Columns&hellip;"
    377381          tooltip="Show, hide and re-order columns"
     382        />
     383        <tbl:button
     384          image="add.png"
     385          onclick="newReporterList()"
     386          title="New reporter list&hellip;"
     387          tooltip="Create a new reporter list from matching wells"
     388          visible="<%=sc.hasPermission(Permission.CREATE, Item.REPORTERLIST)%>"
    378389        />
    379390        <tbl:button

  • trunk/www/views/rawbioassays/rawdata/index.jsp

    r3679 r4305  
    3232  import="net.sf.basedb.core.ItemContext"
    3333  import="net.sf.basedb.core.data.RawData"
     34  import="net.sf.basedb.core.data.ReporterData"
    3435  import="net.sf.basedb.core.RawBioAssay"
    3536  import="net.sf.basedb.core.RawDataType"
    … …  
    126127    redirect = "../../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&subcontext="+rawDataType.getId()+"&context_type=LIST&main_type=OTHER&title=Run+plugin";
    127128  }
     129  else if ("CreateReporterList".equals(cmd))
     130  {
     131    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, rawDataType.getId(), pageContext, defaultContext);
     132    final DataQuery<ReporterData> query = rba.getReporters();
     133    cc.configureQuery(query, true);
     134    cc.setQuery(query);
     135    redirect = "../../../views/reporterlists/index.jsp?ID="+ID+
     136      "&cmd=NewItem&addReporters=1&formId=rawdata&fromContext=RAWDATA&subContext="+rawDataType.getId()+
     137      "&name=" + HTML.urlEncode(rba.getName());
     138  }
    128139  else
    129140  {

  • trunk/www/views/rawbioassays/rawdata/list_rawdata.jsp

    r4302 r4305  
    162162      }
    163163    }
     164    function newReporterList()
     165    {
     166      Table.submitToPopup(formId, 'CreateReporterList', 540, 400);
     167    }
    164168    </script>
    165169  </base:head>
    … …  
    557561          title="Columns&hellip;"
    558562          tooltip="Show, hide and re-order columns"
     563        />
     564        <tbl:button
     565          image="add.png"
     566          onclick="newReporterList()"
     567          title="New reporter list&hellip;"
     568          tooltip="Create a new reporter list from matching spots"
     569          visible="<%=sc.hasPermission(Permission.CREATE, Item.REPORTERLIST)%>"
    559570        />
    560571        <tbl:button

  • trunk/www/views/reporterlists/edit_reporterlist.jsp

    r4301 r4305  
    5151{
    5252  String title = null;
     53  String name = null;
    5354  ReporterList reporterList = null;
    5455  boolean addReporters = false;
    5556  boolean mergeReporterLists = false;
    5657  int numSelectedLists = cc.getSelected().size();
     58  String formId = Values.getString(request.getParameter("formId"), "reporters");
     59  String fromContext = Values.getString(request.getParameter("fromContext"), "REPORTER");
     60  String subContext = request.getParameter("subContext");
    5761
    5862  if (itemId == 0)
    … …  
    6266    addReporters = Values.getBoolean(request.getParameter("addReporters"));
    6367    mergeReporterLists = !addReporters && numSelectedLists > 0;
     68    name = request.getParameter("name");
     69    if (name == null) name = Values.getString(cc.getPropertyValue("name"), "New reporter list");
    6470  }
    6571  else
    6672  {
    6773    reporterList = ReporterList.getById(dc, itemId);
     74    name = reporterList.getName();
    6875    cc.setObject("item", reporterList);
    6976    title = "Edit reporter list -- " + HTML.encodeTags(reporterList.getName());
    … …  
    152159      if (!selectedItems)
    153160      {
    154         selectedItems = window.opener.Table.getSelected('reporters');
     161        selectedItems = window.opener.Table.getSelected('<%=formId%>');
    155162      }
    156163      return selectedItems;
    … …  
    166173    <form action="index.jsp?ID=<%=ID%>" method="post" name="reporterList" onsubmit="return false;">
    167174    <input type="hidden" name="cmd" value="UpdateItem">
    168 
     175    <input type="hidden" name="fromContext" value="<%=fromContext%>">
     176    <%
     177    if (subContext != null)
     178    {
     179      %>
     180      <input type="hidden" name="subContext" value="<%=subContext%>">
     181      <%
     182    }
     183    %>
    169184    <h3 class="docked"><%=title%> <base:help tabcontrol="settings" /></h3>
    170185    <t:tabcontrol id="settings" contentstyle="<%="height: "+(int)(scale*260)+"px;"%>"
    … …  
    176191        <td class="prompt">Name</td>
    177192        <td><input <%=requiredClazz%> type="text" name="name"
    178           value="<%=HTML.encodeTags(reporterList == null ? Values.getString(cc.getPropertyValue("name"), "New reporter list") : reporterList.getName())%>"
     193          value="<%=HTML.encodeTags(name)%>"
    179194          size="40" maxlength="<%=ReporterList.MAX_NAME_LENGTH%>"></td>
    180195      </tr>

  • trunk/www/views/reporterlists/index.jsp

    r4301 r4305  
    139139    {
    140140      rl = ReporterList.getNew(dc);
    141       message = "Reporter list created";
    142141      dc.saveItem(rl);
    143142     
    … …  
    146145      if (which != null)
    147146      {
    148         DataQuery<ReporterData> query = (DataQuery<ReporterData>)sc.getCurrentContext(Item.REPORTER).getQuery();
     147        Item fromContext = Item.valueOf(request.getParameter("fromContext"));
     148        String subContext = Values.getString(request.getParameter("subContext"), "");
     149        DataQuery<ReporterData> query =
     150          (DataQuery<ReporterData>)sc.getCurrentContext(fromContext, subContext).getQuery();
    149151        if ("all".equals(which))
    150152        {
    … …  
    165167          query.setParameter("_selected_", Arrays.asList(itemIds), Type.INT);     
    166168        }
     169        // else -- no modifications to the query mean that we only get the current page
    167170       
    168171        DataResultIterator<ReporterData> result = query.iterate(dc);
    169172        while (result.hasNext())
    170173        {
    171           rl.addReporter(result.next(), null);
     174          ReporterData reporter = result.next();
     175          if (reporter != null) rl.addReporter(reporter, null);
    172176        }
    173177      }
    … …  
    196200        }
    197201      }
     202      message = "Reporter list created with " + rl.getSize() + " reporter(s)";
    198203    }
    199204    else

  • trunk/www/views/reporters/index.jsp

    r4093 r4305  
    272272    cc.configureQuery(query, true);
    273273    cc.setQuery(query);
    274     redirect = "../reporterlists/index.jsp?ID="+ID+"&cmd=NewItem&addReporters=1";
     274    redirect = "../reporterlists/index.jsp?ID="+ID+"&cmd=NewItem&addReporters=1&formId=reporters&fromContext=REPORTER";
    275275  }
    276276  else
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