Changeset 7052


Ignore:
Timestamp:
Jan 11, 2016, 2:40:07 PM (6 years ago)
Author:
Nicklas Nordborg
Message:

Merge pre-3.7 changes to the the trunk.

Location:
trunk
Files:
17 edited

Legend:

Unmodified
Added
Removed
  • trunk

  • trunk/doc/test/roles/index.html

    r6958 r7052  
    22512251    <p>
    22522252   
    2253     It should display one warning for the <b>Experiment A</b> experiment. The warning is
    2254     related to a missing biosurce on the reference sample.
     2253    For the <b>Experiment A</b> experiment, it should display several warnings about missing
     2254    kits and one warning about a missing biosurce on the reference sample.
    22552255    <p>
    22562256    The <b>Affymetrix A</b> experiment gives some more warnings. Most of them are
     
    22992299  </li>
    23002300 
    2301   </ol>
    2302   </li>
    23032301  </ol>
    23042302
  • trunk/src/clients/web/net/sf/basedb/clients/web/PermissionUtil.java

    r6756 r7052  
    186186        Arrays.asList(new Item[]
    187187        {
    188           Item.PROTOCOL, Item.HARDWARE, Item.SOFTWARE,
     188          Item.PROTOCOL, Item.HARDWARE, Item.SOFTWARE, Item.KIT,
    189189          Item.ANNOTATIONTYPE, Item.ANNOTATIONTYPECATEGORY, Item.MIMETYPE,
    190190          Item.REPORTER, Item.REPORTERLIST, Item.REPORTERTYPE, Item.REPORTERCLONETEMPLATE,
  • trunk/src/clients/web/net/sf/basedb/clients/web/plugins/AnyToAnyDataLoader.java

    r6932 r7052  
    4848    @param linkName Name of the any-to-any link (required)
    4949    @param linkType Target item type of the link (optional)
    50     @param propertyPath Property of the target item to load (optional)
     50    @param linkProperty Property of the target item to load (optional)
    5151  */
    5252  @SuppressWarnings("unchecked")
  • trunk/src/core/net/sf/basedb/core/Annotation.java

    r6937 r7052  
    9393    Create a new inherited or cloned annotation.
    9494    @param dc The DbControl object
    95     @param annotationType The annotation type of the new annotation
     95    @param inheritedFrom The annotation to inherit
    9696    @param annotationSet The annotation set of the new annotation
     97    @param clone If the annotation values should be cloned or not
    9798    @see AnnotationSet#getAnnotation(AnnotationType)
    9899    @since 3.6
  • trunk/src/core/net/sf/basedb/core/AnnotationSet.java

    r6940 r7052  
    10441044    inherit by annotation set is no longer supported. Calling
    10451045    this method will be translated to inheriting all individual annotations
    1046     from the annotation set using {@link #inheritAll(AnnotationSet)}
     1046    from the annotation set using {@link #inheritAll(AnnotationSet, boolean)}
    10471047   
    10481048    @param annotationSet The annotation set to inherit
     
    10511051      use permission for the annotation set to inherit
    10521052    @throws InvalidDataException If the annotation set is null
    1053     @deprecated In 3.6, use {@link #inheritAll(AnnotationSet)} instead
     1053    @deprecated In 3.6, use {@link #inheritAll(AnnotationSet, boolean)} instead
    10541054  */
    10551055  @Deprecated
  • trunk/src/core/net/sf/basedb/core/Application.java

    r6721 r7052  
    535535        SystemItems.init();
    536536        Keyring.init();
    537         HibernateUtil.testTransactions();
     537        if (verifySchemaVersion) HibernateUtil.testTransactions();
    538538        RawDataTypes.initPlatforms(null);
    539539 
  • trunk/src/core/net/sf/basedb/core/ClonableProperty.java

    r6428 r7052  
    233233  {
    234234    List<ClonableProperty> mandatory = new ArrayList<ClonableProperty>();
     235    mandatory.add(createFromRegular(EXTERNAL_ID));
    235236    mandatory.add(createFromRegular(ID));
    236237    mandatory.add(createFromRegular(VERSION));
    237     mandatory.add(createFromRegular(EXTERNAL_ID));
    238238    return mandatory;
    239239  }
  • trunk/src/core/net/sf/basedb/core/Kit.java

    r6996 r7052  
    4949    The ID for the sampling kit type, for example a kit
    5050    used when creating a {@link Sample} from a {@link
    51     Biosource}.
     51    BioSource}.
    5252  */
    5353  public static final String SAMPLING = "net.sf.basedb.core.KitType.SAMPLING";
     
    294294    <ul>
    295295    <li>{@link BioMaterial}:s and {@link PhysicalBioAssay}:s using this kit
    296     <li>{@link BioPlateEvents}:s with this kit
     296    <li>{@link BioPlateEvent}:s with this kit
    297297    <li>{@link DerivedBioAssay}: with this kit
    298298    </ul>
  • trunk/src/core/net/sf/basedb/core/Update.java

    r7035 r7052  
    247247    <td>122</td>
    248248    <td>
    249       Added {@link RootRawBioAssayData}. Existing raw bioassay<->Experiment links
     249      Added {@link RootRawBioAssayData}. Existing raw bioassay -- Experiment links
    250250      are moved over to this item.
    251251    </td>
  • trunk/src/core/net/sf/basedb/core/query/ConditionalQueryElement.java

    r7018 r7052  
    3535  @author Nicklas
    3636  @since 3.7
    37   @see Restrictions#conditionalRestriction(Filter, Restriction, Restriction)
     37  @see Restrictions#conditionalRestriction(Filter, Restriction, Restriction, boolean)
    3838*/
    3939public class ConditionalQueryElement
     
    4949    assert ifTrue != null : "ifTrue == null";
    5050    assert ifFalse != null : "ifFalse == null";
    51     this.filter = (Filter<Query>)filter;
     51    this.filter = filter;
    5252    this.ifTrue = ifTrue;
    5353    this.ifFalse = ifFalse;
  • trunk/src/core/net/sf/basedb/core/query/ReturnClassFilter.java

    r7034 r7052  
    3131  with a conditiona restriction or expression as
    3232  created by {@link Restrictions#conditionalRestriction(Filter, Restriction, Restriction, boolean)}
    33   and {@link Expressions#conditionalRestriction(Filter, Expression, Expression, boolean)}
     33  and {@link Expressions#conditionalExpression(Filter, Expression, Expression)}
    3434 
    3535  @author nicklas
  • trunk/src/core/net/sf/basedb/core/snapshot/AnnotationSnapshot.java

    r6962 r7052  
    400400    Get the unit the annotatation values should use for display.
    401401    NOTE! The unit is only available for primary and cloned annotations. Use
    402     {@link #getActualUnit()} or {@link #getInheritedFrom()}.getThisUnit() to get
     402    {@link #getActualUnit(DbControl)} or {@link #getInheritedFrom()}.getThisUnit() to get
    403403    the unit also for inherited annotations.
    404404   
  • trunk/src/core/net/sf/basedb/util/bcrypt/BCrypt.java

    r6906 r7052  
    3131* <p>
    3232* <code>
    33 * String pw_hash = BCrypt.hashpw(plain_password, BCrypt.gensalt()); <br />
     33* String pw_hash = BCrypt.hashpw(plain_password, BCrypt.gensalt()); <br>
    3434* </code>
    3535* <p>
     
    3838* <p>
    3939* <code>
    40 * if (BCrypt.checkpw(candidate_password, stored_hash))<br />
    41 * &nbsp;&nbsp;&nbsp;&nbsp;System.out.println("It matches");<br />
    42 * else<br />
    43 * &nbsp;&nbsp;&nbsp;&nbsp;System.out.println("It does not match");<br />
     40* if (BCrypt.checkpw(candidate_password, stored_hash))<br>
     41* &nbsp;&nbsp;&nbsp;&nbsp;System.out.println("It matches");<br>
     42* else<br>
     43* &nbsp;&nbsp;&nbsp;&nbsp;System.out.println("It does not match");<br>
    4444* </code>
    4545* <p>
     
    4848* <p>
    4949* <code>
    50 * String strong_salt = BCrypt.gensalt(10)<br />
    51 * String stronger_salt = BCrypt.gensalt(12)<br />
     50* String strong_salt = BCrypt.gensalt(10)<br>
     51* String stronger_salt = BCrypt.gensalt(12)<br>
    5252* </code>
    5353* <p>
  • trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/AbstractItemImporter.java

    r6998 r7052  
    675675        // pick out items on which write permission is granted
    676676        List<I> writableItems = new ArrayList<I>();
    677         for (I i : items)
    678         {
    679           if (i.hasPermission(Permission.WRITE))
     677        if (updateExistingItems)
     678        {
     679          // Only check for WRITE permission if we are going to update
     680          for (I i : items)
    680681          {
    681             writableItems.add(i);
     682            if (i.hasPermission(Permission.WRITE))
     683            {
     684              writableItems.add(i);
     685            }
    682686          }
     687        }
     688        else
     689        {
     690          // Pretend we have WRITE permission; we handle the !updateExistingItems later
     691          writableItems.addAll(items);
    683692        }
    684693        if (writableItems.size() == 1)
  • trunk/src/test/net/sf/basedb/test/roles/AnalysisTest.java

    r6372 r7052  
    8282     
    8383      ValidationOptions options = new ValidationOptions();
    84       // Expected, since we never specified a biosource for the reference sample
     84      // Expected, since we never specified a biosource for the reference sample and never kit for any item
    8585      options.setSeverity((ValidationRuleAction)Validator.MISSING_BIOSOURCE, Severity.IGNORE);
     86      options.setSeverity((ValidationRuleAction)Validator.MISSING_KIT, Severity.IGNORE);
    8687      GenericOverview overview = getExperimentOverview(dc, experiment,
    8788        activeProject, options, 0);
  • trunk/www/include/scripts/main-2.js

    r7001 r7052  
    28142814      Doc.addFinalizer(function()
    28152815      {
    2816         element.focus();
    2817         if (autoInit == 'focus-select') element.select();
     2816        setTimeout(function()
     2817          {
     2818            element.focus();
     2819            if (autoInit == 'focus-select') element.select();
     2820          }, 250);
    28182821      });
    28192822    }
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