Changeset 4835


Ignore:
Timestamp:
Mar 24, 2009, 9:22:28 AM (13 years ago)
Author:
Nicklas Nordborg
Message:

Merged patch release 2.10.1 to the trunk.

Location:
trunk
Files:
8 edited

Legend:

Unmodified
Added
Removed
  • trunk/credits.txt

    r4789 r4835  
    2626USA.
    2727
    28 The current BASE team is (at BASE 2.10 release)
     28The current BASE team is (at BASE 2.10.1 release)
    2929
    3030Jari Häkkinen
  • trunk/src/clients/web/net/sf/basedb/clients/web/extensions/menu/MenuItemAction.java

    r4512 r4835  
    2727  An action for extensions to the menu system. The extension point
    2828  will add menu items to the <code>Extensions</code> menu.
    29  
    30   Currently, two menu
    31   subtypes are supported: a real menu item and a menu separator.
    32   Submenus are not supported.
     29  <p>
     30  There are three types of menu items:
     31  <ul>
     32  <li>A regular menu item, which is usually associated with some kind
     33    of action when the user clicks on it.
     34  <li>A separator item. It's just for visual appearance. It is
     35    never associated with any action.
     36  <li>A submenu item, which opens up a submenu when the user
     37    selects it. A submenu must specify a {@link #getSubmenuId()}.
     38    Regular menu items can be put into the submenu item by specifying
     39    the same id for {@link #getMenuId()}.
     40  </ul>
    3341
    3442  @author nicklas
     
    157165   
    158166    /**
    159       A menu item that opens a submenu.
     167      A menu item that opens a submenu. Menu items of this type must
     168      provide a unique value for {@link MenuItemAction#getSubmenuId()}.
     169      A regular menu item can be placed inside a submenu by specifying the
     170      same value for {@link MenuItemAction#getMenuId()}.
    160171    */
    161172    SUBMENU,
  • trunk/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java

    r4822 r4835  
    240240    "itemNotFoundError",
    241241    "Item not found",
    242     "What to do if the plug-in can't find an item with the name or external ID from the file.\n\n"+
     242    "What to do if the plug-in can't find an item with the name or external ID from the file." +
     243    "This also include the case when name or external ID is unspecified in the file.\n\n"+
    243244    "skip = Skip the current data line and continue\n"+
    244245    "fail = Stop with an error message",
     
    753754    {
    754755      items = new HashSet<NewAnnotations>();
    755       // The 'name' parameter can also query against the external ID
    756       itemQuery.setParameter("nameOrId", searchParameterType.parseString(nameOrId), searchParameterType);
    757       List<?> result = itemQuery.list(dc);
    758       if (result.isEmpty())
    759       {
    760         // No item with specified name/external ID was found
    761         if (!ignoreNotFoundItems)
    762         {
    763           throw new ItemNotFoundException(itemType +
    764             "[" + searchProperty + "=" + nameOrId + "]");
    765         }
    766         else
    767         {
    768           numItemNotFound++;
    769         }
    770       }
    771       if (result.size() > 1 && failIfMultipleFoundItems)
    772       {
    773         throw new BaseException("Found " + result.size() + " " + itemType.toString().toLowerCase() +
    774           " with " + searchProperty + "=" + nameOrId);
    775       }
    776       for (Object item : result)
    777       {
    778         // Add each item that was found to the cache
    779         items.add(new NewAnnotations((Annotatable)item));
    780       }
    781       itemCache.put(nameOrId, items);
     756     
     757      if (nameOrId != null)
     758      {
     759        // The 'name' parameter can also query against the external ID
     760        itemQuery.setParameter("nameOrId", searchParameterType.parseString(nameOrId), searchParameterType);
     761        List<?> result = itemQuery.list(dc);
     762        if (result.isEmpty())
     763        {
     764          // No item with specified name/external ID was found
     765          if (!ignoreNotFoundItems)
     766          {
     767            throw new ItemNotFoundException(itemType +
     768              "[" + searchProperty + "=" + nameOrId + "]");
     769          }
     770          else
     771          {
     772            numItemNotFound++;
     773          }
     774        }
     775        if (result.size() > 1 && failIfMultipleFoundItems)
     776        {
     777          throw new BaseException("Found " + result.size() + " " + itemType.toString().toLowerCase() +
     778            " with " + searchProperty + "=" + nameOrId);
     779        }
     780        for (Object item : result)
     781        {
     782          // Add each item that was found to the cache
     783          items.add(new NewAnnotations((Annotatable)item));
     784        }
     785        itemCache.put(nameOrId, items);
     786      }
     787      else if (!ignoreNotFoundItems)
     788      {
     789        throw new ItemNotFoundException(itemType + "[" + searchProperty + " has no value in file]");
     790      }
     791      else
     792      {
     793        numItemNotFound++;
     794      }
    782795    }
    783796   
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java

    r4736 r4835  
    4141import net.sf.basedb.core.BioPlate;
    4242import net.sf.basedb.core.BioSource;
    43 import net.sf.basedb.core.BioWell;
    4443import net.sf.basedb.core.BooleanParameterType;
    4544import net.sf.basedb.core.DataFileType;
  • trunk/www/lims/arraybatches/index.jsp

    r4587 r4835  
    264264    cc.configureQuery(query, true);
    265265    cc.setQuery(query);
    266     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+hybridizations";
     266    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+array+batches";
    267267  }
    268268  else if ("ExportItem".equals(cmd))
     
    270270    // Run an export plugin in single-item context
    271271    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    272     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+hybridization";
     272    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+array+batch";
    273273  }
    274274  else if ("ImportItems".equals(cmd))
     
    279279    cc.configureQuery(query, true);
    280280    cc.setQuery(query);
    281     redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+hybrydizations";
     281    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+array+batches";
    282282  }
    283283  else if ("ImportItem".equals(cmd))
     
    285285    // Run an import plugin in single-item context
    286286    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    287     redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+hybridization";
     287    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+array+batch";
    288288  }
    289289  else if ("RunListPlugin".equals(cmd))
  • trunk/www/lims/arrayslides/index.jsp

    r4587 r4835  
    312312    cc.configureQuery(query, true);
    313313    cc.setQuery(query);
    314     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+hybridizations";
     314    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+array+slides";
    315315  }
    316316  else if ("ExportItem".equals(cmd))
     
    318318    // Run an export plugin in single-item context
    319319    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    320     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+hybridization";
     320    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+array+slide";
    321321  }
    322322  else if ("ImportItems".equals(cmd))
     
    327327    cc.configureQuery(query, true);
    328328    cc.setQuery(query);
    329     redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+hybrydizations";
     329    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+array+slides";
    330330  }
    331331  else if ("ImportItem".equals(cmd))
     
    333333    // Run an import plugin in single-item context
    334334    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    335     redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+hybridization";
     335    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+array+slide";
    336336  }
    337337  else if ("RunListPlugin".equals(cmd))
  • trunk/www/views/experiments/index.jsp

    r4630 r4835  
    303303    cc.configureQuery(query, true);
    304304    cc.setQuery(query);
    305     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+raw+bioassays";
     305    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+experiments";
    306306  }
    307307  else if ("ExportItem".equals(cmd))
     
    309309    // Run an export plugin in single-item context
    310310    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    311     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+raw+bioassay";
     311    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+experiment";
    312312  }
    313313  else if ("ImportItems".equals(cmd))
     
    318318    cc.configureQuery(query, true);
    319319    cc.setQuery(query);
    320     redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+raw+bioassays";
     320    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+experiments";
    321321  }
    322322  else if ("ImportItem".equals(cmd))
     
    324324    // Run an import plugin in single-item context
    325325    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    326     redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+raw+bioassay";
     326    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+experiment";
    327327  }
    328328  else if ("RunListPlugin".equals(cmd))
  • trunk/www/views/scans/index.jsp

    r4587 r4835  
    268268    cc.configureQuery(query, true);
    269269    cc.setQuery(query);
    270     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+raw+bioassays";
     270    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Export+scans";
    271271  }
    272272  else if ("ExportItem".equals(cmd))
     
    274274    // Run an export plugin in single-item context
    275275    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    276     redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+raw+bioassay";
     276    redirect = "../../common/export/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Export+scan";
    277277  }
    278278  else if ("ImportItems".equals(cmd))
     
    283283    cc.configureQuery(query, true);
    284284    cc.setQuery(query);
    285     redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+raw+bioassays";
     285    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=LIST&title=Import+scans";
    286286  }
    287287  else if ("ImportItem".equals(cmd))
     
    289289    // Run an import plugin in single-item context
    290290    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
    291     redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+raw+bioassay";
     291    redirect = "../../common/import/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&title=Import+scan";
    292292  }
    293293  else if ("RunListPlugin".equals(cmd))
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