Changeset 7587

Timestamp:

Feb 6, 2019, 10:41:56 AM (5 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 3.14.1 to the trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• src/core/net/sf/basedb/core/Extract.java (modified) (1 diff)
• src/core/net/sf/basedb/core/HibernateUtil.java (modified) (5 diffs)
• www/biomaterials/extracts/extracts.js (modified) (2 diffs)
• www/biomaterials/extracts/index.jsp (modified) (3 diffs)
• www/biomaterials/extracts/list_extracts.jsp (modified) (5 diffs)
• www/biomaterials/extracts/view_extract.jsp (modified) (3 diffs)
• www/common/annotations/annotate.jsp (modified) (4 diffs)
• www/common/annotations/list_annotations.jsp (modified) (4 diffs)
• www/my_base/user/settings.jsp (modified) (2 diffs)
• www/views/derivedbioassays/edit_bioassay.jsp (modified) (1 diff)

trunk/src/core/net/sf/basedb/core/Extract.java

@@ -361 +361 @@
   }
 
-
+  /**
+    Get a query that returns all derived bioassays created from this 
+    extract.
+    @return An {@link ItemQuery} object
+    @since 3.14.1
+  */
+  public ItemQuery<DerivedBioAssay> getDerivedBioAssays()
+  {
+    ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
+    query.joinPermanent(Hql.innerJoin("extract", Item.EXTRACT.getAlias()));
+    query.restrictPermanent(
+      Restrictions.eq(
+        Hql.alias(Item.EXTRACT.getAlias()),
+        Hql.entity(this)
+      )
+    );
+    return query;
+  }
+
+  /**
+    Get a query that returns all raw bioassays created from this 
+    extract.
+    @return An {@link ItemQuery} object
+    @since 3.14.1
+  */
+  public ItemQuery<RawBioAssay> getRawBioAssays()
+  {
+    ItemQuery<RawBioAssay> query = RawBioAssay.getQuery();
+    query.joinPermanent(Hql.innerJoin("parentExtract", Item.EXTRACT.getAlias()));
+    query.restrictPermanent(
+      Restrictions.eq(
+        Hql.alias(Item.EXTRACT.getAlias()),
+        Hql.entity(this)
+      )
+    );
+    return query;
+  }
+  
   // -------------------------------------------
   /*

trunk/src/core/net/sf/basedb/core/HibernateUtil.java

@@ -291 +291 @@
     }
     String dbUrl = Config.getString("db.url", "");
-    checkJdbcDriver(dbUrl);
+    String dbUser = Config.getString("db.username", "");
+    String dbPassword = Config.getString("db.password", "");
+    checkJdbcDriver(dbUrl, dbUser, dbPassword);
     
     Properties baseConfig = new Properties();
     baseConfig.setProperty("hibernate.dialect", dialect);
     baseConfig.setProperty("hibernate.connection.url", dbUrl);
-    baseConfig.setProperty("hibernate.connection.username", Config.getString("db.username", ""));
-    baseConfig.setProperty("hibernate.connection.password", Config.getString("db.password", ""));
+    baseConfig.setProperty("hibernate.connection.username", dbUser);
+    baseConfig.setProperty("hibernate.connection.password", dbPassword);
     return baseConfig;
   }
@@ -304 +306 @@
     Check that a JDBC driver is registered and try to load a driver if not.
   */
-  private static void checkJdbcDriver(String dbUrl)
+  private static void checkJdbcDriver(String dbUrl, String dbUser, String dbPassword)
   {
     Driver driver = null;
@@ -320 +322 @@
       ServiceLoader<Driver> s = ServiceLoader.load(Driver.class);
       Iterator<Driver> it = s.iterator();
-      while (it.hasNext())
+      while (driver == null && it.hasNext())
       {
         Driver d = it.next();
@@ -335 +337 @@
               "; version=" + d.getMajorVersion() + "." + d.getMinorVersion()+
               "; acceptsURL="+acceptUrl);
-          if (acceptUrl && driver == null)
-          {
-            driver = d;
-          }
+          if (acceptUrl) driver = d;
         }
       }
@@ -346 +345 @@
       throw new ConfigurationException("Could not find a suitable JDBC driver for URL: " + dbUrl);
     }
+    
+    Properties props = new Properties();
+    props.setProperty("user", Config.getString("db.username", ""));
+    props.setProperty("password", Config.getString("db.password", ""));
+
+    try (Connection c = driver.connect(dbUrl, props))
+    {
+      if (!c.isValid(5))
+      {
+        throw new ConfigurationException("Could not connect to database: " + dbUrl);
+      }
+    }
+    catch (SQLException ex)
+    {
+      throw new ConfigurationException("Could not connect to database: " + dbUrl + " (" + ex.getMessage() + ")", ex);
+    }
+    
     log.info("Accepted JDBC driver " + driver.getClass().getName() + 
         "; version=" + driver.getMajorVersion() + "." + driver.getMinorVersion());

trunk/www/biomaterials/extracts/extracts.js

@@ -141 +141 @@
       Buttons.addClickHandler(element, extracts.newExtract);
     }
+    else if (autoInit == 'new-derived-bioassay')
+    {
+      Buttons.addClickHandler(element, extracts.newDerivedBioAssay);
+    }
     else if (autoInit == 'new-raw-bioassay')
     {
@@ -155 +159 @@
     Items.newItem('EXTRACT', '&extract_id='+extractId);
   }
+  
+  /*
+    Create a new derived bioassay with the current extract as the parent
+  */
+  extracts.newDerivedBioAssay = function(event)
+  {
+    var extractId = Data.int(event.currentTarget, 'item-id');
+    Items.newItem('DERIVEDBIOASSAY', '&extract_id='+extractId);
+  }
+
   
   /*

trunk/www/biomaterials/extracts/index.jsp

@@ -39 +39 @@
   import="net.sf.basedb.core.Tag"
   import="net.sf.basedb.core.PhysicalBioAssay"
+  import="net.sf.basedb.core.DerivedBioAssay"
   import="net.sf.basedb.core.RawBioAssay"
   import="net.sf.basedb.core.ItemSubtype"
@@ -99 +100 @@
     cc.setObject("export.formatter.&childCreationEvents(event.physicalBioAssay.name)", new NameableFormatter());
     cc.setObject("export.formatter.&childCreationEvents(event.bioMaterial.name)", new NameableFormatter());
+    cc.setObject("export.formatter.&derivedBioAssays(name)", new NameableFormatter());
     cc.setObject("export.formatter.&rawBioAssays(name)", new NameableFormatter());
     cc.setObject("export.formatter.parentType", new ItemTypeFormatter());
@@ -125 +127 @@
     cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ParentBioMaterialEventSourceLoader());
     
+    // Child derived bioassays
+    final ItemQuery<DerivedBioAssay> derivedBioAssayQuery = DerivedBioAssay.getQuery();
+    derivedBioAssayQuery.restrict(Restrictions.eq(Hql.property("extract"), Expressions.parameter(restrictionParameter)));
+    derivedBioAssayQuery.order(Orders.asc(Hql.property("name")));
+    derivedBioAssayQuery.include(cc.getInclude());
+    cc.setObject("export.dataloader.&derivedBioAssays(name)", new ItemQueryLoader(derivedBioAssayQuery, restrictionParameter));
+
     // Child raw bioassays
     final ItemQuery<RawBioAssay> rawBioAssayQuery = RawBioAssay.getQuery();

trunk/www/biomaterials/extracts/list_extracts.jsp

@@ -32 +32 @@
   import="net.sf.basedb.core.PhysicalBioAssay"
   import="net.sf.basedb.core.RawBioAssay"
+  import="net.sf.basedb.core.DerivedBioAssay"
   import="net.sf.basedb.core.BioPlate"
   import="net.sf.basedb.core.BioMaterialEvent"
@@ -129 +130 @@
   final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
   final boolean createBioAssayPermission = sc.hasPermission(Permission.CREATE, Item.PHYSICALBIOASSAY);
+  final boolean createDerivedBioAssayPermission = sc.hasPermission(Permission.CREATE, Item.DERIVEDBIOASSAY);
   final boolean createRawBioAssayPermission = sc.hasPermission(Permission.CREATE, Item.RAWBIOASSAY);
 
-  // Child bioassays
+  // Child physical bioassays
   final ItemQuery<PhysicalBioAssay> bioAssayQuery = PhysicalBioAssay.getQuery();
   bioAssayQuery.join(Hql.innerJoin("creationEvent", "ce"));
@@ -138 +140 @@
   bioAssayQuery.order(Orders.asc(Hql.property("name")));
   bioAssayQuery.include(cc.getInclude());
+
+  // Child derived bioassays
+  final ItemQuery<DerivedBioAssay> derivedAssayQuery = DerivedBioAssay.getQuery();
+  derivedAssayQuery.restrict(Restrictions.eq(Hql.property("extract"), Hql.entityParameter("extract", Item.EXTRACT)));
+  derivedAssayQuery.order(Orders.asc(Hql.property("name")));
+  derivedAssayQuery.include(cc.getInclude());
 
   // Child raw bioassays
@@ -387 +395 @@
         title="Physical bioassays"
         property="&childCreationEvents(event.physicalBioAssay.name)"
+        datatype="string"
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef
+        id="derivedBioAssays"
+        title="Derived bioassays"
+        property="&derivedBioAssays(name)"
         datatype="string"
         filterable="true"
@@ -925 +941 @@
                   %>
                 </tbl:cell>
+                <tbl:cell column="derivedBioAssays">
+                  <%                  
+                  try
+                  {
+                    derivedAssayQuery.setEntityParameter("extract", item);
+                    String separator = "";
+                    for (DerivedBioAssay dba : derivedAssayQuery.list(dc))
+                    {
+                      out.write(separator);
+                      if (mode.hasPropertyLink())
+                      {
+                        out.write(Base.getLinkedName(ID, dba, false, mode.hasEditLink()));
+                      }
+                      else
+                      {
+                        out.write(HTML.encodeTags(dba.getName()));
+                      }
+                      separator = ", ";
+                    }
+                  }
+                  catch (Throwable t)
+                  {
+                    %>
+                    <div class="error"><%=t.getMessage()%></div>
+                    <%
+                  }
+                  %>
+                  <base:icon
+                    id="<%="newDerivedBioAssay."+itemId%>"
+                    image="add.png" 
+                    subclass="auto-init"
+                    data-auto-init="new-derived-bioassay"
+                    data-item-id="<%=itemId %>"
+                    tooltip="Create new derived bioassay from this extract" 
+                    visible="<%=mode.hasEditLink() && createDerivedBioAssayPermission && usePermission %>"
+                  />
+                </tbl:cell>
                 <tbl:cell column="rawBioAssays">
                   <%                  

trunk/www/biomaterials/extracts/view_extract.jsp

@@ -41 +41 @@
   import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.BioWell"
+  import="net.sf.basedb.core.RawDataType"
+  import="net.sf.basedb.core.RawBioAssay"
+  import="net.sf.basedb.core.DerivedBioAssay"
   import="net.sf.basedb.core.MultiPermissions"
   import="net.sf.basedb.core.ItemSubtype"
@@ -440 +443 @@
       childQuery.order(Orders.asc(Hql.property("bm", "name")));
       ResultList<BioMaterialEventSource> children = childQuery.list(dc);
+      
+      ItemQuery<DerivedBioAssay> dbaQuery = extract.getDerivedBioAssays();
+      dbaQuery.include(Include.ALL);
+      dbaQuery.order(Orders.asc(Hql.property("name")));
+      ItemResultList<DerivedBioAssay> derivedBioAssays = dbaQuery.list(dc);
+      
+      ItemQuery<RawBioAssay> rbaQuery = extract.getRawBioAssays();
+      rbaQuery.include(Include.ALL);
+      rbaQuery.order(Orders.asc(Hql.property("name")));
+      ItemResultList<RawBioAssay> rawBioAssays = rbaQuery.list(dc);
+
+      int numChildren = children.size() + derivedBioAssays.size() + rawBioAssays.size();
       %>
       <base:section 
         id="childSection" 
-        title="<%="Child items (" + children.size() + ")"%>"
+        title="<%="Child items (" + numChildren + ")"%>"
         context="<%=cc%>"
         >
         <%
-        if (children.size() == 0)
+        if (numChildren == 0)
         {
           %>
@@ -537 +552 @@
                 <%
               }
-              %>            
+              for (DerivedBioAssay dba : derivedBioAssays)
+              {
+                ItemSubtype subtype = null;
+                try
+                {
+                  subtype = dba.getItemSubtype();
+                }
+                catch (PermissionDeniedException ex)
+                {}
+                %>
+                <tbl:row>
+                  <tbl:cell column="name"><base:icon 
+                      image="deleted.png" 
+                      tooltip="This item has been scheduled for deletion" 
+                      visible="<%=dba.isRemoved()%>"
+                    /><%=Base.getLinkedName(ID, dba, false, true)%></tbl:cell>
+                  <tbl:cell column="type">
+                    <%
+                    if (subtype != null)
+                    {
+                      %>
+                      <%=Base.getLinkedName(ID, subtype, false, true)%> <span class="itemsubtype">(<%=dba.getType() %>)</span>
+                      <%
+                    }
+                    else
+                    {
+                      %>
+                      <%=dba.getType()%>
+                      <%
+                    }
+                    %>
+                  </tbl:cell>
+                  <tbl:cell column="quantity"></tbl:cell>
+                  <tbl:cell column="description"><%=HTML.encodeTags(dba.getDescription())%></tbl:cell>
+                </tbl:row>
+                <%
+              }
+              for (RawBioAssay rba : rawBioAssays)
+              {
+                RawDataType rawtype = null;
+                try
+                {
+                  rawtype = rba.getRawDataType();
+                }
+                catch (PermissionDeniedException ex)
+                {}
+                %>
+                <tbl:row>
+                  <tbl:cell column="name"><base:icon 
+                      image="deleted.png" 
+                      tooltip="This item has been scheduled for deletion" 
+                      visible="<%=rba.isRemoved()%>"
+                    /><%=Base.getLinkedName(ID, rba, false, true)%></tbl:cell>
+                  <tbl:cell column="type">
+                    <%=rawtype.getName()%> <span class="itemsubtype">(<%=rba.getType() %>)</span>
+                  </tbl:cell>
+                  <tbl:cell column="quantity"></tbl:cell>
+                  <tbl:cell column="description"><%=HTML.encodeTags(rba.getDescription())%></tbl:cell>
+                </tbl:row>
+                <%
+              }
+              %>
               </tbl:rows>
             </tbl:data>

trunk/www/common/annotations/annotate.jsp

@@ -39 +39 @@
   import="net.sf.basedb.core.BioPlateType"
   import="net.sf.basedb.core.BioPlate"
+  import="net.sf.basedb.core.RawBioAssay"
+  import="net.sf.basedb.core.RawDataType"
+  import="net.sf.basedb.core.RawDataTypes"
   import="net.sf.basedb.core.AnnotationSet"
   import="net.sf.basedb.core.Annotation"
@@ -157 +160 @@
       if (subtype == null) selectedCategoryName = bpt.getName();
     }
+    else if (item instanceof RawBioAssay)
+    {
+      RawDataType rdt = ((RawBioAssay)item).getRawDataType();
+      selectedCategoryName = rdt.getName();
+    }
     if (subtype != null) selectedCategoryName = subtype.getName();
   }
@@ -191 +199 @@
   final Set<AnnotationTypeCategory> allCategories = 
     new TreeSet<AnnotationTypeCategory>(new NameableComparator(false));
+  
+  // Load all ItemSubtypes that are NOT related to the current item type
+  // We need this to get rid of annotation type categories that are not intended
+  // for the current item type
+  Set<String> excludedCategories = new HashSet<>();
+  ItemQuery<ItemSubtype> query = ItemSubtype.getQuery(null);
+  query.restrict(Restrictions.neq(Hql.property("itemType"), Expressions.integer(itemType.getValue())));
+  for (ItemSubtype s : query.list(dc))
+  {
+    if (Annotatable.class.isAssignableFrom(s.getMainItemType().getItemClass()))
+    {
+      excludedCategories.add(s.getName());
+    }
+  }
+  // Raw data types are also used as subtypes
+  if (itemType != Item.RAWBIOASSAY)
+  {
+    for (RawDataType rdt : RawDataTypes.getRawDataTypes())
+    {
+      excludedCategories.add(rdt.getName());
+    }
+  }
   
   // Load existing annotations
@@ -553 +583 @@
           {
             boolean selected = category.getName().equals(selectedCategoryName);
+            if (!selected && excludedCategories.contains(category.getName())) continue;
             %>
             <option value="<%=category.getId()%>"

trunk/www/common/annotations/list_annotations.jsp

@@ -23 +23 @@
   @version 2.0
 --%>
-<%@page import="java.util.Collections"%>
-<%@page import="net.sf.basedb.util.units.UnitConverter"%>
 <%@ page pageEncoding="UTF-8" session="false"
   import="net.sf.basedb.core.SessionControl"
@@ -42 +40 @@
   import="net.sf.basedb.core.BioPlate"
   import="net.sf.basedb.core.BioPlateType"
+  import="net.sf.basedb.core.RawDataType"
+  import="net.sf.basedb.core.RawBioAssay"
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultList"
@@ -56 +56 @@
   import="net.sf.basedb.clients.web.util.HTML"
   import="net.sf.basedb.util.NameableComparator"
+  import="net.sf.basedb.util.units.UnitConverter"
   import="net.sf.basedb.util.formatter.Formatter"
   import="net.sf.basedb.util.formatter.PrefixSuffixFormatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
   import="net.sf.basedb.util.Values"
+  import="java.util.Collections"
   import="java.util.ArrayList"
   import="java.util.List"
@@ -165 +167 @@
       subtype = bpt.getItemSubtype();
       if (subtype == null) selectedCategoryName = bpt.getName();
+    }
+    else if (item instanceof RawBioAssay)
+    {
+      RawDataType rdt = ((RawBioAssay)item).getRawDataType();
+      selectedCategoryName = rdt.getName();
     }
     if (subtype != null) selectedCategoryName = subtype.getName();

trunk/www/my_base/user/settings.jsp

@@ -72 +72 @@
   final boolean writePermission = user.hasPermission(Permission.RESTRICTED_WRITE);
   final String ifDisabled = writePermission ? "" : "disabled";
-  final String passwordDisabled = writePermission && Application.isUsingInternalAuthentication() ? 
-    "" : "disabled";
+  final String passwordDisabled = writePermission ? "" : "disabled";
   dc.detachItem(user);
   sc.setSessionSetting("user", user);
@@ -206 +205 @@
       <t:tab id="password" title="Password" helpid="userpreferences.password">
         <table class="fullform input100">
-        <% if (!Application.isUsingInternalAuthentication() && writePermission)
-        {
-          %>
-          <tr>
-            <td colspan="2">
-            <div class="messagecontainer error">Base is using external authentication. Password cannot be changed here.</div>
-            </td>
-          </tr>
-          <%
-        }
-        %>
         <tr>
           <th>Login</th>

trunk/www/views/derivedbioassays/edit_bioassay.jsp

@@ -147 +147 @@
     }
 
+    int extractId = Values.getInt(request.getParameter("extract_id"));
+    if (extractId != 0)
+    {
+      currentExtract = Extract.getById(dc, extractId);
+    }
+    else if (cc.getPropertyFilter("extract.name") != null)
+    {
+      currentExtract = Base.getFirstMatching(dc, Extract.getQuery(), "name", cc.getPropertyFilter("extract.name"));
+    }
+
     if (currentSubtypeId == 0) 
     {