Changeset 7494

Timestamp:

Jun 4, 2018, 8:42:46 AM (5 years ago)

Author:

Nicklas Nordborg

Message:

Merged patch release 3.12.3 to the trunk.

Location:

trunk

Files:

• . (modified) (1 prop)
• config/dist/base.config (modified) (1 diff)
• src/core/net/sf/basedb/core/AnnotationSimpleRestriction.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/SessionControl.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/GeoLocation.java (modified) (1 diff)
• src/core/net/sf/basedb/util/formatter/PropertyFilterFormatter.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/loader/DerivedBioAssayLoader.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/overview/loader/RawBioAssayLoader.java (modified) (4 diffs)
• www/common/import/index.jsp (modified) (1 diff)
• www/common/plugin/configure.jsp (modified) (2 diffs)
• www/common/plugin/parse_file.jsp (modified) (10 diffs)
• www/include/scripts/main-2.js (modified) (1 diff)

trunk/config/dist/base.config

@@ -267 +267 @@
 # ===================
 
-# URL to a 'freegeoip' server. Use {IP} as a placeholder for
-# the IP address. The service should return a JSON data object.
-# Software for running your own server can be downloaded from 
-# https://github.com/fiorix/freegeoip
-# If no service is specified, location lookup will be disabled
-geolocation.freegeoip = http://freegeoip.net/json/{IP}
+# URL to the 'ipstack' (previously 'freegeoip') server. Use {IP} as a
+# placeholder for the IP address. The service should return a JSON 
+# data object. Before it can be used you need to register and receive
+# an API key. See https://ipstack.com/ for more information.
+# Replace [API_KEY] in the URL below and uncomment the setting to 
+# activate geolocation lookup.
+# geolocation.freegeoip = http://api.ipstack.com/{IP}?access_key=[API_KEY]&output=json
 
 # A template URL for displaying a map with a marker on a specified location

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

@@ -113 +113 @@
   
   /**
+    Creates a new annotation restriction for a specific <code>valueType</code>.
+    The restriction is with a list of values.
+    
+    @param alias The alias of a joined item where the annotations are
+      located or null to use the root entity of the query
+    @param annotationType The annotation type to use in the query
+      @param operator The operator, it must be one of the expression
+      operators, EQ, NEQ, etc., not a boolean operator, AND, OR, etc.
+      @param values The list of values that should be used in the query, they must be of the 
+      correct value type for the annotation as defined by the 
+      {@link AnnotationType#getValueType()} property.
+    @param options Options that specify which annotations to consider when searching
+      @throws InvalidDataException If any of the parameters are null
+      or not follow the rules above
+    @since 3.12.3
+  */
+  public AnnotationSimpleRestriction(String alias, AnnotationType annotationType, Operator operator, List<Object> values, 
+    Options options)
+    throws InvalidDataException
+  {
+    super(alias, annotationType, options);
+    if (operator == null) throw new InvalidUseOfNullException("operator");
+    if (values == null) throw new InvalidUseOfNullException("values");
+    if (!operator.isExpressionOperator())
+    {
+      throw new InvalidDataException("Invalid operator for expression: "+operator);
+    }
+    for (Object obj : values)
+    {
+      if (obj != null && !valueType.isCorrectType(obj) && !(valueType.isNumerical() && obj instanceof Number))
+      {
+        throw new InvalidDataException("Value '"+obj+"' is a "+
+          obj.getClass()+", not a "+valueType);
+      }
+    }
+    this.operator = operator;
+    this.value = null;
+    this.values = values;
+  }
+
+  
+  /**
     @since 2.4
     @deprecated in 3.5; Use {@link #AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean, boolean)} instead
@@ -163 +205 @@
   /**
     @since 3.5
-    @deprecated In 3.11, use {@link #AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options)} instead
+    @deprecated In 3.11, use {@link #AnnotationSimpleRestriction(String, AnnotationType, Operator, List, AnnotationRestriction.Options)} instead
   */
   @Deprecated

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

@@ -350 +350 @@
   }
   
-  GeoLocation getLocation()
-  {
-    if (!locationLoaded)
+  GeoLocation getLocation(AuthenticationMethod authMeth)
+  {
+    if (!locationLoaded && authMeth != null && authMeth != AuthenticationMethod.INTERNAL)
     {
       locationLoaded = true;
@@ -895 +895 @@
     device.setLastUsed(now);
     device.setLastRemoteId(getRemoteId());
-    GeoLocation loc = getLocation();
+    GeoLocation loc = getLocation(authUser.getAuthenticationMethod());
     if (loc == null) loc = new GeoLocation(); // To force 'null' on the location fields
     device.setLocation(loc.toString());
@@ -1084 +1084 @@
     sessionData.setLoginComment(comment);
     sessionData.setRemoteId(getRemoteId());
-    GeoLocation loc = getLocation();
+    GeoLocation loc = getLocation(authenticationMethod);
     if (loc != null)
     {

trunk/src/core/net/sf/basedb/util/GeoLocation.java

@@ -240 +240 @@
       
       HttpEntity entity = response.getEntity();
-      Header contentType = entity.getContentType();
-      if (contentType != null && !"application/json".equals(contentType.getValue()))
-      {
-        throw new RuntimeException("Unexpected content type: "+contentType.getValue());
+      Header contentTypeHeader = entity.getContentType();
+      String contentType = contentTypeHeader != null ? contentTypeHeader.getValue() : null;
+      if (contentType != null && !contentType.contains("application/json"))
+      {
+        throw new RuntimeException("Unexpected content type: "+contentType);
       }
       

trunk/src/core/net/sf/basedb/util/formatter/PropertyFilterFormatter.java

@@ -112 +112 @@
       sb.append(")");
     }
-    else if (property.equals("itemSubtype"))
-    {
-      // Special handling to display name of subtype
+    else if (property.equals("bioWell.row") || property.equals("bioWell.column"))
+    {
+      WellCoordinateFormatter formatter = new WellCoordinateFormatter(property.equals("bioWell.row"));
       sb.append(property).append(" ").append(operator).append(" ");
-      List<Object> subtypes = filter.getValuesAsObjects();
-      if (subtypes.size() > 1) sb.append("(");
-      if (subtypes.size() == 0) sb.append("null");
+      List<Object> selected = filter.getValuesAsObjects();
+      if (selected.size() > 1) sb.append("(");
+      if (selected.size() == 0) sb.append("null");
       String sep = "";
-      for (Object id : subtypes)
+      for (Object index : selected)
       {
         sb.append(sep);
         sep = ", ";
-        sb.append(nameOfItem(dc, Item.ITEMSUBTYPE, (Integer)id, true));
-      }
-      if (subtypes.size() > 1) sb.append(")");
+        sb.append(formatter.format((Integer)index));
+      }
+      if (selected.size() > 1) sb.append(")");
+    }
+    else if (property.equals("parentType"))
+    {
+      sb.append(property).append(" ").append(operator).append(" ");
+      List<Object> selected = filter.getValuesAsObjects();
+      if (selected.size() > 1) sb.append("(");
+      if (selected.size() == 0) sb.append("null");
+      String sep = "";
+      for (Object index : selected)
+      {
+        sb.append(sep);
+        sep = ", ";
+        sb.append(Item.fromValue((Integer)index).toString());
+      }
+      if (selected.size() > 1) sb.append(")");
     }
     else
     {
-      if (property.startsWith("&") || property.startsWith("@") || property.startsWith("!"))
-      {
-        property = property.substring(1);
-      }
-      sb.append(property).append(" ").append(operator).append(" ");
-      if (operator.isListOperator() && value != null)
-      {
-        appendListOfValues(sb, value, quote);
+      Item nameOfItemType = null;
+      if (property.equals("itemSubtype") || property.endsWith(".itemSubtype"))
+      {
+        // Special handling to display name of subtype
+        nameOfItemType = Item.ITEMSUBTYPE;
+      }
+      else if (property.equals("platform"))
+      {
+        // Special handling to display name of platform
+        nameOfItemType = Item.PLATFORM;
+      }
+      if (nameOfItemType != null)
+      {
+        sb.append(property).append(" ").append(operator).append(" ");
+        List<Object> itemIds = filter.getValuesAsObjects();
+        if (itemIds.size() > 1) sb.append("(");
+        if (itemIds.size() == 0) sb.append("null");
+        String sep = "";
+        for (Object id : itemIds)
+        {
+          sb.append(sep);
+          sep = ", ";
+          sb.append(nameOfItem(dc, nameOfItemType, (Integer)id, true));
+        }
+        if (itemIds.size() > 1) sb.append(")");
       }
       else
       {
-        if (filter.getValueType().isTemporal())
-        {
-          value = dateFormatter.format((Date)Type.DATE.parseString(value));
-        }
-        sb.append(quote).append(value).append(quote);
+        if (property.startsWith("&") || property.startsWith("@") || property.startsWith("!"))
+        {
+          property = property.substring(1);
+        }
+        sb.append(property).append(" ").append(operator).append(" ");
+        if (operator.isListOperator() && value != null)
+        {
+          appendListOfValues(sb, value, quote);
+        }
+        else
+        {
+          if (filter.getValueType().isTemporal())
+          {
+            value = dateFormatter.format((Date)Type.DATE.parseString(value));
+          }
+          sb.append(quote).append(value).append(quote);
+        }
       }
     }

trunk/src/core/net/sf/basedb/util/overview/loader/DerivedBioAssayLoader.java

@@ -50 +50 @@
 import net.sf.basedb.util.overview.OverviewUtil;
 import net.sf.basedb.util.overview.Validator;
+import net.sf.basedb.util.overview.filter.BasicItemFilter;
 import net.sf.basedb.util.overview.filter.ItemTypeFilter;
 import net.sf.basedb.util.overview.node.ChildNodeDirection;
@@ -157 +158 @@
   protected void loadPropertyChildNodes(DbControl dc, OverviewContext context, Node bioAssayNode)
   {
-    getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, bioAssayNode);
+    Extract e = getExtract((DerivedBioAssay)bioAssayNode.getItem());
+    if (e == null || bioAssayNode.getFirstParent(new BasicItemFilter(e)) == null)
+    {
+      // Only load the extract if it is not already a parent node
+      getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, bioAssayNode);
+    }
     getNodeLoader(context, Item.ANNOTATION).createPropertyNode(dc, context, bioAssayNode);
     getNodeLoader(context, Item.FILESETMEMBER).createPropertyNode(dc, context, bioAssayNode);
@@ -281 +287 @@
     NodeFactory<DerivedBioAssay> nf = getNodeFactory(dc, context);
     Node folderNode = null;
+    // Load derived bioassays linked to the 'extract' if:
+    // they have no parent bioassay OR
+    // the parent bioassay has no parent extract OR
+    // the parent bioassay has a different parent extract
     ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
     query.restrict(Restrictions.eq(Hql.property("extract"), Hql.entity(extract)));
     query.join(Hql.leftJoin("parents", "parent"));
-    query.restrict(Restrictions.eq(Hql.alias("parent"), null));
+    query.join(Hql.leftJoin("parent", "extract", "parentExtract", null, false));
+    query.restrict(
+      Restrictions.or(
+        Restrictions.eq(Hql.alias("parent"), null),
+        Restrictions.eq(Hql.alias("parentExtract"), null),
+        Restrictions.neq(Hql.alias("parentExtract"), Hql.entity(extract))
+        ));
+    query.setDistinct(true); // left joins may create multiple hits for items with more than one parent
     context.initQuery(query, "name");
     ItemResultIterator<DerivedBioAssay> it = query.iterate(dc);

trunk/src/core/net/sf/basedb/util/overview/loader/RawBioAssayLoader.java

@@ -47 +47 @@
 import net.sf.basedb.util.overview.NodeAttribute;
 import net.sf.basedb.util.overview.OverviewContext;
+import net.sf.basedb.util.overview.filter.BasicItemFilter;
 import net.sf.basedb.util.overview.filter.ItemTypeFilter;
 import net.sf.basedb.util.overview.node.ChildNodeDirection;
@@ -169 +170 @@
   protected void loadPropertyChildNodes(DbControl dc, OverviewContext context, Node rawBioAssayNode)
   {
-    getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, rawBioAssayNode);
+    Extract e = getExtract((RawBioAssay)rawBioAssayNode.getItem());
+    if (e == null || rawBioAssayNode.getFirstParent(new BasicItemFilter(e)) == null)
+    {
+      // Only load the extract if it is not already a parent node
+      getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, rawBioAssayNode);
+    }
     getNodeLoader(context, Item.ANNOTATION).createPropertyNode(dc, context, rawBioAssayNode);
     getNodeLoader(context, Item.FILESETMEMBER).createPropertyNode(dc, context, rawBioAssayNode);
@@ -235 +241 @@
     NodeFactory<RawBioAssay> nf = getNodeFactory(dc, context);
     Node folderNode = null;
+    // Load raw bioassays linked to the 'extract' if:
+    // they have no parent bioassay OR
+    // the parent bioassay has no parent extract OR
+    // the parent bioassay has a different parent extract
     ItemQuery<RawBioAssay> query = RawBioAssay.getQuery();
     query.restrict(Restrictions.eq(Hql.property("parentExtract"), Hql.entity(extract)));
-    query.restrict(Restrictions.eq(Hql.property("parentBioAssay"), null));
+    query.join(Hql.leftJoin("parentBioAssay", "parent"));
+    query.join(Hql.leftJoin("parent", "extract", "parentExtract", null, false));
+    query.restrict(
+        Restrictions.or(
+          Restrictions.eq(Hql.alias("parent"), null),
+          Restrictions.eq(Hql.alias("parentExtract"), null),
+          Restrictions.neq(Hql.alias("parentExtract"), Hql.entity(extract))
+          ));
     context.initQuery(query, "name");
     ItemResultIterator<RawBioAssay> it = query.iterate(dc);
@@ -253 +270 @@
   }
   
+  /**
+    Get the extract that is associated with the current raw bioassay
+    @return The extract or null if none was found
+  */
+  private Extract getExtract(RawBioAssay bioAssay)
+  {
+    Extract extract = null;
+    try
+    {
+      extract = bioAssay.getParentExtract();
+    }
+    catch (PermissionDeniedException ex)
+    {}
+    return extract;
+  }
+
   private Set<Integer> getExtractChain(DbControl dc, Node node)
   {

trunk/www/common/import/index.jsp

@@ -189 +189 @@
 
     cc.setObject("auto-detected-file", f);
+    cc.setObject("last-file-charset", charset);
     int matches = plugins.size();
     if (matches == 0)

trunk/www/common/plugin/configure.jsp

@@ -99 +99 @@
     }
   }
+  
+  // Special handling for "charset" parameter to make it match the auto-selected file
+  if (currentContext != null && Parameters.CHARSET_PARAMETER.equals(pp.getName()))
+  {
+    Object charset = currentContext.getObject("last-file-charset");
+    if (charset != null) values = Collections.singletonList(charset);
+  }
+  
   // Then, we check the parameters default value
   if ((values == null || values.size() == 0) && pp.getDefaultValue() != null)
@@ -123 +131 @@
         try
         {
-          values.add(File.getById(dc, cc.getId()).getPath().toString());
+          File file = File.getById(dc, cc.getId());
+          values.add(file.getPath().toString());
+          if (currentContext != null && file.getCharacterSet() != null)
+          {
+            currentContext.setObject("last-file-charset", file.getCharacterSet());
+          }
         }
         catch (Throwable t)

trunk/www/common/plugin/parse_file.jsp

@@ -24 +24 @@
   @version 2.0
 --%>
-<%@page import="org.json.simple.JSONObject"%>
 <%@ page pageEncoding="UTF-8" session="false"
   contentType="text/html; charset=UTF-8"  
@@ -49 +48 @@
   import="java.io.InputStream"
   import="org.json.simple.JSONArray"
+  import="org.json.simple.JSONObject"
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -173 +173 @@
   %>
   <base:page type="iframe" title="Test with file">
-  <base:head scripts="tabcontrol-2.js,~parse_file.js" styles="table.css,tabcontrol.css" />
+  <base:head scripts="tabcontrol-2.js,~parse_file.js" styles="table.css,tabcontrol.css">
+    <style>
+    #fileData td
+    {
+      white-space: nowrap;
+      max-width: 20em;
+      min-width: 4em;
+      overflow: hidden;
+      text-overflow: ellipsis;
+    }
+    #fileData td:first-child
+    {
+      font-weight: bold;
+    }
+    .skipped
+    {
+      padding: 1px 2px 1px 2px;
+      color: #777777;
+      font-style: italic;
+    }
+    </style>
+  </base:head>
   <base:body>
   <div class="absolutefull bottomborder">
@@ -216 +237 @@
       <div class="itemlist" style="<%=messages.size()==0 ? "" : "border-top-width: 1px;"%>">
         <div class="data">
-        <table style="border: 0;">
+        <table style="border: 0;" id="fileData">
           <thead class="bg-filled-100">
           <tr>
@@ -234 +255 @@
         int rowClassIndex = 0;
 
-        while (currentLine <= maxLines && currentLine < headerLines)
+        while (currentLine < maxLines && currentLine < headerLines)
         {
           FlatFileParser.Line line = parser.getLine(currentLine);
           linePatterns.add(Pattern.quote(line.line()));
           String[] data = null;
+          int numMoreColumns = 0;
           if (line.type() == FlatFileParser.LineType.HEADER)
           {
@@ -246 +268 @@
           {
             data = parser.trimQuotes(splitter.split(line.line(), 99));
+            if (data.length == 99)
+            {
+              numMoreColumns = splitter.split(line.line()).length - 99;
+            }
           }
           else
@@ -254 +280 @@
           <tr class="<%=rowclass[rowClassIndex]%> highlight">
             <td class="cell"><%=line.lineNo()%></td>
-            <td class="cell"><%=data.length%></td>
+            <td class="cell"><%=data.length+numMoreColumns%></td>
             <td class="cell"><%=line.type()%></td>
             <td class="cell">
@@ -290 +316 @@
         {
           if (lastLine == FlatFileParser.LineType.DATA) parser.nextData();
-          while (currentLine <= maxLines && parser.hasMoreData())
+          while (currentLine < maxLines && parser.hasMoreData())
           {
             FlatFileParser.Data data = parser.nextData();
@@ -298 +324 @@
               %>
               <tr>
-                <td class="error" colspan="103">
+                <td class="skipped bg-filled-100" colspan="103">
                 Skipped <%=parser.getNumSkippedLines()%> lines 
                 (<%=parser.getIgnoredLines()%> ignored; <%=parser.getUnknownLines()%> unknown)
@@ -320 +346 @@
               </td>
               <%
-              for (int i = 0; i < data.columns(); ++i)
+              for (int i = 0; i < data.columns() && i < 99; ++i)
               {
                 %>

trunk/www/include/scripts/main-2.js

@@ -4551 +4551 @@
       optionDiv.optionIndex = i;
       optionDiv.innerHTML = options[i];
-      options[i].div = optionDiv;
       mainDiv.appendChild(optionDiv);
     }