Changeset 7874


Ignore:
Timestamp:
Oct 22, 2020, 8:21:45 AM (3 years ago)
Author:
Nicklas Nordborg
Message:

Merged pre-3.17-changes to the trunk.

Location:
trunk
Files:
1 deleted
12 edited
1 copied

Legend:

Unmodified
Added
Removed

  • trunk

  • trunk/credits.txt

    r7794 r7874  
    11$Id$
    22
    3 The current BASE team is (at BASE 3.16 release)
     3The current BASE team is (at BASE 3.17 release)
    44{{{
    55Jari Häkkinen

  • trunk/doc/3rd-party-components.txt

    r7825 r7874  
    107107
    108108More info : https://dev.mysql.com/downloads/connector/j/
    109 Version   : 8.0.19
     109Version   : 8.0.22
    110110License   : GPLv2 (mysql-connector-LICENSE.txt)
    111 Jar files : mysql-connector-java-8.0.19.jar
     111Jar files : mysql-connector-java-8.0.22.jar
    112112
    113113

  • trunk/src/clients/web/net/sf/basedb/clients/web/extensions/list/AnyLinkColumnActionFactory.java

    r7855 r7874  
    5757
    5858 
    59   @SuppressWarnings("unchecked")
     59  @SuppressWarnings({"unchecked", "rawtypes"})
    6060  @Override
    6161  public ListColumnAction<BasicItem, Object>[] getActions(InvokationContext<? super ListColumnAction<BasicItem, Object>> context)

  • trunk/src/clients/web/net/sf/basedb/clients/web/extensions/list/RelatedItemColumnActionFactory.java

    r7840 r7874  
    6060
    6161 
    62   @SuppressWarnings("unchecked")
     62  @SuppressWarnings({"unchecked", "rawtypes"})
    6363  @Override
    6464  public ListColumnAction<Annotatable, Object>[] getActions(InvokationContext<? super ListColumnAction<Annotatable, Object>> context)

  • trunk/src/clients/web/net/sf/basedb/clients/web/formatter/AutoLinkFormatter.java

    r7855 r7874  
    3535
    3636  * Files are linked with {@link Base#getLinkedFile(String, File, boolean, boolean, boolean, String)}
     37    and with a {@link FileViewerUtil} if it is available
    3738  * Nameable items are linked with {@link Base#getLinkedName(String, Nameable, boolean, boolean)}
    38   * Other items are linked with {@link Base#getLink(String, String, Item, int, boolean)
     39  * Other items are linked with {@link Base#getLink(String, String, Item, int, boolean)}
    3940 
    4041 

  • trunk/src/core/net/sf/basedb/util/AnyToAnyLinkStatistics.java

    r7853 r7874  
    150150      Set the maximum number of items to use for gathering the statistics.
    151151      The default value is 500. A higher value may affect performance.
    152       @param maxRandomSamples
    153152    */
    154153    public void setMaxRandomSamples(int maxRandomSamples)

  • trunk/src/core/net/sf/basedb/util/parser/FlatFileParser.java

    r7832 r7874  
    20112011    protected String fixString(String value)
    20122012    {
    2013       // TODO - In Java 11 we can use String.strip() which also handles other white-space than "space"
    2014       if (value != null && trimWhiteSpace) value = value.trim();     
     2013      if (value != null && trimWhiteSpace) value = value.strip();     
    20152014     
    20162015      return value == null ||

  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/AnyToAnyImporter.java

    r7849 r7874  
    4949import net.sf.basedb.core.Job;
    5050import net.sf.basedb.core.Metadata;
     51import net.sf.basedb.core.Nameable;
    5152import net.sf.basedb.core.Permission;
    5253import net.sf.basedb.core.PluginParameter;

  • trunk/src/test/net/sf/basedb/test/roles/AnalysisTest.java

    r7052 r7874  
    4848import net.sf.basedb.util.overview.Validator;
    4949import net.sf.basedb.util.overview.Failure;
    50 import net.sf.basedb.util.overview.extensions.ValidationRuleAction;
    5150
    5251/**
    … …  
    8281     
    8382      ValidationOptions options = new ValidationOptions();
    84       // Expected, since we never specified a biosource for the reference sample and never kit for any item
    85       options.setSeverity((ValidationRuleAction)Validator.MISSING_BIOSOURCE, Severity.IGNORE);
    86       options.setSeverity((ValidationRuleAction)Validator.MISSING_KIT, Severity.IGNORE);
     83      // Expected, since we never specified a biosource for the reference sample and never kit for any item or files for protocols
     84      options.setSeverity(Validator.MISSING_BIOSOURCE, Severity.IGNORE);
     85      options.setSeverity(Validator.MISSING_KIT, Severity.IGNORE);
     86      options.setSeverity(Validator.MISSING_FILE, Severity.IGNORE);
    8787      GenericOverview overview = getExperimentOverview(dc, experiment,
    8888        activeProject, options, 0);
    8989     
    9090      // Expected, since the Affymetrix experiment is using a different raw data type
    91       options.setSeverity((ValidationRuleAction)Validator.NONDEFAULT_RAWDATATYPE, Severity.IGNORE);
    92       options.setSeverity((ValidationRuleAction)Validator.MISSING_HARDWARE, Severity.IGNORE);
    93       options.setSeverity((ValidationRuleAction)Validator.MISSING_PROTOCOL, Severity.IGNORE);
    94       options.setSeverity((ValidationRuleAction)Validator.NONMATCHING_SPOTCOUNT, Severity.IGNORE);
     91      options.setSeverity(Validator.NONDEFAULT_RAWDATATYPE, Severity.IGNORE);
     92      options.setSeverity(Validator.MISSING_HARDWARE, Severity.IGNORE);
     93      options.setSeverity(Validator.MISSING_PROTOCOL, Severity.IGNORE);
     94      options.setSeverity(Validator.NONMATCHING_SPOTCOUNT, Severity.IGNORE);
    9595      GenericOverview affyOverview = getExperimentOverview(dc, affyExperiment,
    9696        activeProject, options, 2);
    9797     
    98       options.setSeverity((ValidationRuleAction)Validator.MISSING_ARRAYSLIDE, Severity.IGNORE);
    99       options.setSeverity((ValidationRuleAction)Validator.MISSING_TAG, Severity.IGNORE);
     98      options.setSeverity(Validator.MISSING_ARRAYSLIDE, Severity.IGNORE);
     99      options.setSeverity(Validator.MISSING_TAG, Severity.IGNORE);
    100100      // Sequence experiment overview
    101101      GenericOverview seqOverview = getExperimentOverview(dc, seqExperiment,

  • trunk/www/common/columns/add_linkeditem_column.jsp

    r7853 r7874  
    6464    <div class="content">
    6565      <table class="fullform input100 bottomborder">
    66       <tr>
    67         <th></th>
    68         <td>
    69           <select name="presets" id="presets" style="width: 25em;">
    70           <option value="">- presets -
    71           <%
    72           for (AnyToAnyLinkStatistics stat : stats)
    73           {
    74             String name = HTML.encodeTags(stat.getLinkName());
    75             String targetType = stat.getTargetType().name();
     66      <%
     67      if (stats.size() > 0)
     68      {
     69        %>
     70        <tr>
     71          <th></th>
     72          <td>
     73            <select name="presets" id="presets" style="width: 25em;">
     74            <option value="">- presets -
     75            <%
     76            for (AnyToAnyLinkStatistics stat : stats)
     77            {
     78              String name = HTML.encodeTags(stat.getLinkName());
     79              String targetType = stat.getTargetType().name();
     80              %>
     81              <option data-linkname="<%=name%>" data-targettype="<%=targetType%>"><%=name%> [<%=targetType%>]
     82              <%
     83            }
    7684            %>
    77             <option data-linkname="<%=name%>" data-targettype="<%=targetType%>"><%=name%> [<%=targetType%>]
    78             <%
    79           }
    80           %>
    81           </select>
    82         </td>
    83       </tr>
     85            </select>
     86          </td>
     87        </tr>
     88        <%
     89      }
     90      %>
    8491      <tr>
    8592        <th style="border-top-width: 0;">Link name</th>

  • trunk/www/include/styles/table.css

    r7851 r7874  
    225225  float: left;
    226226  content: '›';
    227   color: #999999;
     227  color: #666666;
    228228}
    229229
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