Changeset 3653


Ignore:
Timestamp:
Aug 10, 2007, 12:59:24 PM (14 years ago)
Author:
Jari Häkkinen
Message:

Merged log:trunk#3581:3649 into the wwebservices branch.

Location:
branches/webservices
Files:
2 deleted
137 edited
50 copied

Legend:

Unmodified
Added
Removed
  • branches/webservices/config/dist/extended-properties.xml

    r3581 r3653  
    179179      type="string"
    180180      length="255"
    181     />   
     181      >
     182      <link
     183        regexp=".+"
     184        url="callto://{value}"
     185      />
     186    </property>
    182187  </class>
    183188</extended-properties>
  • branches/webservices/config/dist/raw-data-types.xml

    r3533 r3653  
    232232      column="flags"
    233233      type="int"
     234      averagemethod="none"
    234235    />
    235236    <property
     
    31683169    </intensity-formula>
    31693170  </raw-data-type>
     3171  <raw-data-type
     3172    id="illumina"
     3173    channels="1"
     3174    name="Illumina"
     3175    table="RawDataIllumina">
     3176    <property
     3177      name="MIN_Signal"
     3178      title="MIN_Signal"
     3179      description="Minimum intensity of the gene in the group."
     3180      column="minSignal"
     3181      type="float"     
     3182    />
     3183    <property
     3184      name="AVG_Signal"
     3185      title="AVG_Signal"
     3186      description="Average intensity of the gene in the group."
     3187      column="avgSignal"
     3188      type="float"     
     3189    />
     3190    <property
     3191      name="MAX_Signal"
     3192      title="MAX_Signal"
     3193      description="Maximum intensity of the gene in the group."
     3194      column="maxSignal"
     3195      type="float"     
     3196    />
     3197    <property
     3198      name="NARRAYS"
     3199      title="NARRAYS"
     3200      description="Number of arrays in the group."
     3201      column="narrays"
     3202      type="int"     
     3203    />
     3204    <property
     3205      name="ARRAY_STDEV"
     3206      title="ARRAY_STDEV"
     3207      description="Standard deviation associated with array-to-array variability within the group (undefined when the group contains a single array)."
     3208      column="arrayStdDev"
     3209      type="float"     
     3210    />
     3211    <property
     3212      name="BEAD_STDEV"
     3213      title="BEAD_STDEV"
     3214      description="Average standard deviation associated with bead-to-bead variability for the arrays in the group."
     3215      column="beadStdDev"
     3216      type="float"     
     3217    />
     3218    <property
     3219      name="Avg_NBEADS"
     3220      title="Avg_NBEADS"
     3221      description="Average number of beads per bead type representing probes for the gene."
     3222      column="avgNBeads"
     3223      type="int"     
     3224    />
     3225    <property
     3226      name="Detection"
     3227      title="Detection"
     3228      description="p-value computed from the background model characterizing chance that the target sequence signal was distinguishable from the negative controls."
     3229      column="detection"
     3230      type="float"     
     3231    />
     3232    <intensity-formula
     3233      name="avgSignal"
     3234      title="Average signal"
     3235      description="Average signal as determined by BeadStudio software."
     3236      >
     3237      <formula
     3238        channel="1"
     3239        expression="raw('AVG_Signal')"
     3240      />
     3241    </intensity-formula>
     3242  </raw-data-type>
    31703243</raw-data-types>
    31713244
  • branches/webservices/credits.txt

    r3533 r3653  
    2626
    2727
    28 The current BASE team is (at BASE 2.3 release)
     28The current BASE team is (at BASE 2.4 release)
    2929
    3030Johan Enell
     
    4141Samuel Andersson
    4242Micha Bayer
     43Jeremy Davis-Turak
    4344Johan Enell
    4445Michael Green
  • branches/webservices/data/plugin_configfile.xml

    r3133 r3653  
    881881    </parameter>
    882882  </configuration>
     883  <configuration pluginClassName="net.sf.basedb.plugins.PackedFileExporter">
     884    <configname>Zip archive (.zip)</configname>
     885    <description>Compress the selected files/directories and put them in a ZIP file.</description>
     886    <parameter>
     887      <name>packer</name>
     888      <label>Packer class</label>
     889      <description>Enter the name of the class that is responsible for packing the files. It must be a class that implements the FilePacker interface.</description>
     890      <class>java.lang.String</class>
     891      <value>net.sf.basedb.util.zip.ZipFilePacker</value>
     892    </parameter>
     893  </configuration>
     894  <configuration pluginClassName="net.sf.basedb.plugins.PackedFileExporter">
     895    <configname>TAR archive (.tar)</configname>
     896    <description>Collect the selected files/directories into a TAR file (not compressed).</description>
     897    <parameter>
     898      <name>packer</name>
     899      <label>Packer class</label>
     900      <description>Enter the name of the class that is responsible for packing the files. It must be a class that implements the FilePacker interface.</description>
     901      <class>java.lang.String</class>
     902      <value>net.sf.basedb.util.zip.TarFilePacker</value>
     903    </parameter>
     904  </configuration>
     905  <configuration pluginClassName="net.sf.basedb.plugins.PackedFileExporter">
     906    <configname>GZipped TAR archive (.tar.gz)</configname>
     907    <description>Collect the selected files/directoris into a TAR file and compress it with GZIP.</description>
     908    <parameter>
     909      <name>packer</name>
     910      <label>Packer class</label>
     911      <description>Enter the name of the class that is responsible for packing the files. It must be a class that implements the FilePacker interface.</description>
     912      <class>java.lang.String</class>
     913      <value>net.sf.basedb.util.zip.GzipFilePacker</value>
     914    </parameter>
     915  </configuration>
     916  <configuration pluginClassName="net.sf.basedb.plugins.PackedFileExporter">
     917    <configname>BZipped TAR archive (.tar.bz2)</configname>
     918    <description>Collect the selected files/directoris into a TAR file and compress it with BZIP2.</description>
     919    <parameter>
     920      <name>packer</name>
     921      <label>Packer class</label>
     922      <description>Enter the name of the class that is responsible for packing the files. It must be a class that implements the FilePacker interface.</description>
     923      <class>java.lang.String</class>
     924      <value>net.sf.basedb.util.zip.Bzip2FilePacker</value>
     925    </parameter>
     926  </configuration>
    883927</configfile>
  • branches/webservices/doc/src/docbook/appendix/base.config.xml

    r3533 r3653  
    575575      </listitem>
    576576    </varlistentry>
     577    <varlistentry>
     578      <term><property>plugins.autounload</property></term>
     579      <listitem>
     580        <para>
     581          Enable this setting to let BASE detect if a plug-in JAR file is changed
     582          and automatically load and use the new code instead of the old code.
     583          This setting is useful for plug-in developers since they don't have to
     584          restart the webserver each time the plug-in is recompiled.
     585          <itemizedlist>
     586            <listitem>
     587              <simpara>
     588                <userinput>true,yes,1</userinput>
     589                to enable
     590              </simpara>
     591            </listitem>
     592            <listitem>
     593              <simpara>
     594                <userinput>false,no,0</userinput>
     595                to disable (default if no value is specified)
     596              </simpara>
     597            </listitem>
     598          </itemizedlist>
     599        </para>
     600      </listitem>
     601    </varlistentry>
    577602    </variablelist>
    578603  </simplesect>
  • branches/webservices/doc/src/docbook/appendix/extended_properties.xml

    r3334 r3653  
    3030  <title>extended-properties.xml reference</title>
    3131 
    32   <para>
    33     This document is only available in the old format.
    34     See <ulink url="http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html"
    35       >http://base.thep.lu.se/chrome/site/doc/admin/extended-properties.html</ulink>.
    36   </para>
    37 
     32 
     33  <bridgehead>What is extended-properties.xml?</bridgehead>
     34
     35  <para>
     36    The <filename>extended-properties.xml</filename> file is a configuration
     37    file for customizing some of the tables in the BASE database.
     38    It is located in the <filename>&lt;basedir&gt;/www/WEB-INF/classes</filename>
     39    directory. Only a limited number of tables support this feature, the most important
     40    one is the table for storing reporter information.
     41  </para>
     42
     43  <para>
     44    The default <filename>extended-properties.xml</filename> that ships
     45    with BASE is biased towards the BASE 1.2 setup for 2-spotted microarray
     46    data. If you want your BASE installation to be configured differently we
     47    recommend that you do it before the first initialisation of the database.
     48    It is possible to change the configuration of an existing BASE installation but it
     49    may require manual updates to the database. Follow this procedure:
     50  </para>
     51
     52  <orderedlist>
     53  <listitem>
     54    <para>
     55    Shut down the BASE web server. If you have installed job agents you should shut
     56    down them as well.
     57    </para>
     58  </listitem>
     59 
     60  <listitem>
     61    <para>
     62    Modify the <filename>extended-properties.xml</filename> file. If you have installed
     63    job agents, make sure they all have the same version as the web server.
     64    </para>
     65  </listitem>
     66 
     67  <listitem>
     68    <para>
     69    Run the <filename>updatedb.sh</filename> script. New
     70    columns will automatically be created, but the script can't delete columns that
     71    have been removed, or modify columns that have changed datatype. You will have to
     72    do these kind of changes by manually executing SQL against your database. Check your
     73    database documentation for information about SQL syntax.
     74    </para>
     75   
     76    <tip>
     77      <title>Create a parallell installation</title>
     78      <para>
     79      You can always create a new temporary parallell installation to check
     80      what the table generated by installation script looks like. Compare the
     81      new table to the existing one and make sure they match.
     82      </para>
     83    </tip>
     84  </listitem>
     85 
     86  <listitem>
     87    <para>
     88    Start up the BASE web server and any job agents, if any, again.
     89    </para>
     90  </listitem>
     91 
     92  </orderedlist>
     93
     94  <tip>
     95    <title>Start with few columns</title>
     96    <para>
     97    It is better to start with too few columns, since it is easier to add
     98    more columns than it is to remove columns that are not needed.
     99    </para>
     100  </tip>
     101 
     102  <bridgehead>Sample extended properties setups</bridgehead>
     103 
     104  <itemizedlist>
     105  <listitem>
     106    <para>
     107    After installing BASE the default <filename>extended-properties.xml</filename>
     108    is located in the <filename>&lt;basedir&gt;/www/WEB-INF/classes</filename> directory.
     109    This setup is biased towards the BASE 1.2 setup for 2-spotted cDNA arrays.
     110    If you are migrating from BASE 1.2 you need to use the default setup.
     111    </para>
     112  </listitem>
     113 
     114  <listitem>
     115    <para>
     116    A <filename>minimalistic_extended-properties.xml</filename> setup which doesn't
     117    define any extra columns at all. This file
     118    can be found in the <filename>&lt;basedir&gt;/misc/config</filename> directory,
     119    and should be used if it is not known what reporter data will be stored in the
     120    database. The addition of more columns later is straightforward.
     121    </para>
     122  </listitem>
     123  </itemizedlist>
     124
     125
     126  <bridgehead>Format of the extended-properties.xml file</bridgehead>
     127  <para>
     128    The <filename>extended-properties.xml</filename> is an XML file.
     129    The following example will serve as a description of the format:
     130  </para>
     131 
     132  <programlisting>
     133&lt;?xml version="1.0" ?&gt;
     134&lt;!DOCTYPE extended-properties SYSTEM "extended-properties.dtd"&gt;
     135&lt;extended-properties&gt;
     136   &lt;class name="ReporterData"&gt;
     137      &lt;property
     138         name="extra1"
     139         column="extra1"
     140         title="Extra property"
     141         type="string"
     142         length="255"
     143         null="true"
     144         update="true"
     145         insert="true"
     146         averagemethod="max"
     147         description="An extra property for all reporters"
     148      &gt;
     149      &lt;link
     150         regexp=".*"
     151         url="http://www.myexternaldb.com/find?{value}"
     152      /&gt;
     153      &lt;/property&gt;
     154   &lt;/class&gt;
     155&lt;/extended-properties&gt;
     156</programlisting>
     157 
     158  <para>
     159    Each table that can be customized is represented by a <sgmltag class="starttag">class</sgmltag>
     160    tag. The value of the <sgmltag>name</sgmltag> attribute is the name of the Java class
     161    that handles the information in that table. In the case of reporters
     162    the class name is <constant>ReporterData</constant>.
     163  </para>
     164 
     165  <para>
     166    Each <sgmltag class="starttag">class</sgmltag> tag may contain one or more
     167    <sgmltag class="starttag">property</sgmltag> tags, each one describing a single
     168    column in the table. The possible attributes of the <sgmltag class="starttag">property</sgmltag>
     169    tag are:
     170  </para>
     171 
     172    <informaltable frame="all">
     173    <tgroup cols="3" align="left">
     174      <colspec colname="attribute" align="left" />
     175      <colspec colname="required" />
     176      <colspec colname="comment" />
     177      <thead>
     178        <row>
     179          <entry>Attribute</entry>
     180          <entry>Required</entry>
     181          <entry>Comment</entry>
     182        </row>
     183      </thead>
     184      <tbody>
     185        <row>
     186          <entry>name</entry>
     187          <entry>yes</entry>
     188          <entry>
     189            A unique name (within the class) of the extra property.
     190            The name must only contain letters, numbers and underscores but the first character
     191            can't be a number. The name is used to identify the extra column in the Java code
     192            and in the Query API.
     193          </entry>
     194        </row>
     195        <row>
     196          <entry>column</entry>
     197          <entry>yes</entry>
     198          <entry>
     199            The name of the database column. This value must be unique within the
     200            class. Valid names depends on the database, but it should be safe
     201            to follow the same rules as for the <sgmltag>name</sgmltag> attribute.
     202            In most cases, it makes sense to use the same value for both the
     203            <sgmltag>name</sgmltag> and <sgmltag>column</sgmltag> attributes.
     204          </entry>
     205        </row>
     206        <row>
     207          <entry>title</entry>
     208          <entry>no</entry>
     209          <entry>
     210            The title of the extra property as it is displayed in client applications.
     211            If not specified the value of the <sgmltag>name</sgmltag> attrbiute is used.
     212          </entry>
     213        </row>
     214        <row>
     215          <entry>description</entry>
     216          <entry>no</entry>
     217          <entry>
     218            A longer (but still short!) description of the extra property which can be
     219            used in client applications to provide help.
     220          </entry>
     221        </row>
     222        <row>
     223          <entry>type</entry>
     224          <entry>yes</entry>
     225          <entry>
     226            The data type of the column. Allowed values are:
     227            <itemizedlist>
     228            <listitem>
     229              <simpara>int</simpara>
     230            </listitem>
     231            <listitem>
     232              <simpara>long</simpara>
     233            </listitem>
     234            <listitem>
     235              <simpara>float</simpara>
     236            </listitem>
     237            <listitem>
     238              <simpara>double</simpara>
     239            </listitem>
     240            <listitem>
     241              <simpara>boolean</simpara>
     242            </listitem>
     243            <listitem>
     244              <simpara>string</simpara>
     245            </listitem>
     246            <listitem>
     247              <simpara>date</simpara>
     248            </listitem>
     249            </itemizedlist>
     250           
     251            <para>
     252              Note that the given types are converted into the most appropriate database
     253              column type by Hibernate.
     254            </para>
     255          </entry>
     256        </row>
     257        <row>
     258          <entry>length</entry>
     259          <entry>no</entry>
     260          <entry>
     261            If the column is a string type, this is the maximum length that can
     262            be stored in the database. If no value is given, 255 is assumed.
     263          </entry>
     264        </row>
     265        <row>
     266          <entry>null</entry>
     267          <entry>no</entry>
     268          <entry>
     269            If the column should allow <constant>null</constant> values or not.
     270            Allowed values are <constant>true</constant> (default) and
     271            <constant>false</constant>.
     272          </entry>
     273        </row>
     274        <row>
     275          <entry>insert</entry>
     276          <entry>no</entry>
     277          <entry>
     278            If valus for this property should be inserted into the database or not.
     279            Allowed values are <constant>true</constant> (default) and
     280            <constant>false</constant>.
     281          </entry>
     282        </row>
     283        <row>
     284          <entry>update</entry>
     285          <entry>no</entry>
     286          <entry>
     287            If valus for this property should be updated in the database or not.
     288            Allowed values are <constant>true</constant> (default) and
     289            <constant>false</constant>.
     290          </entry>
     291        </row>
     292        <row>
     293          <entry>averagable</entry>
     294          <entry>no</entry>
     295          <entry>
     296            <emphasis>This attribute has been deprecated and replaced by the
     297            <sgmltag>averagemethod</sgmltag> attribute!</emphasis>
     298           
     299            <para>
     300              If it makes sense to calculate the average of a set of values
     301              for this property or not. By default, all numerical columns are
     302              averagable. For non-numerical columns this attribute is ignored.
     303            </para>
     304          </entry>
     305        </row>
     306        <row>
     307          <entry>averagemethod</entry>
     308          <entry>no</entry>
     309          <entry>
     310            The method to use when calculating the average of a set of values.
     311            This attribute replaces the <sgmltag>averagable</sgmltag> attribute.
     312            The following values can be used:
     313             
     314            <itemizedlist>
     315            <listitem>
     316              <simpara>
     317              <constant>none</constant>: average values are not supported
     318              (default for non-numerical columns)
     319              </simpara>
     320            </listitem>
     321            <listitem>
     322              <simpara>
     323              <constant>arithmetic_mean</constant>: calculate the arithmetic mean
     324              (default for numerical columns; not supported for non-numerical columns)
     325              </simpara>
     326            </listitem>
     327            <listitem>
     328              <simpara>
     329              <constant>geometric_mean</constant>: calculate the geometric mean
     330              (not supported for non-numerical columns)
     331              </simpara>
     332            </listitem>
     333            <listitem>
     334              <simpara>
     335              <constant>min</constant>: use the minimum value of the values in the set
     336              </simpara>
     337            </listitem>
     338            <listitem>
     339              <simpara>
     340              <constant>max</constant>: use the maximum value of the values in the set
     341              </simpara>
     342            </listitem>
     343            </itemizedlist>
     344             
     345          </entry>
     346        </row>
     347      </tbody>
     348    </tgroup>
     349    </informaltable>
     350 
     351  <para>
     352    Each <sgmltag class="starttag">property</sgmltag> tag may contain zero or more
     353    <sgmltag class="starttag">link</sgmltag> tags that can be used by client
     354    application to provide clickable links to other databases. Each
     355    <sgmltag class="starttag">link</sgmltag> has a <sgmltag>regexp</sgmltag>
     356    and an <sgmltag>url</sgmltag> attribute. If the regular expression matches
     357    the value a link will be created, otherwise not. The order of the
     358    <sgmltag class="starttag">link</sgmltag> tags are important, since only
     359    the first one that matches is used. The <sgmltag>url</sgmltag> attribute may
     360    contain the string <constant>{value}</constant> which will be replaced by the
     361    actual value when the link is generated.
     362  </para>
     363 
     364  <note>
     365    <para>
     366    If the link contains the character <constant>&amp;</constant> it must be
     367    escaped as <constant>&amp;amp;</constant>. For example, to link to a Unigene
     368    entry:
     369    </para>
     370    <programlisting>
     371&lt;link
     372   regexp="\w+\.\d+"
     373   url="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&amp;amp;term={value}[ClusterID]"
     374/&gt;
     375</programlisting>
     376  </note>
     377
     378 
    38379</appendix>
    39380
  • branches/webservices/doc/src/docbook/appendix/incompatible.xml

    r3533 r3653  
    7979      old behaviour use <code>ch(1) == 'NULL'</code>.
    8080    </para>
     81   
     82    <bridgehead>Parsing strings into numeric values</bridgehead>
     83    <para>
     84      The <methodname>Type.parseString(String)</methodname> method for
     85      <constant>Type.FLOAT</constant> and <constant>Type.DOUBLE</constant>
     86      has changed it's behaviour for <constant>NaN</constant>
     87      and <constant>Infinity</constant> values. The methods used to
     88      return <constant>Float.NaN</constant>, <constant>Float.NEGATIVE_INFINITY</constant>,
     89      <constant>Float.POSITIVE_INFINITY</constant> or the corresponding
     90      <classname>Double</classname> values. Since databases doesn't like
     91      these special values and eventually most values will go into the database,
     92      the <methodname>parseString</methodname> method now returns <constant>null</constant>
     93      instead.
     94    </para>
     95   
     96    <bridgehead>Extended properties and raw data types</bridgehead>
     97    <para>
     98      We have added validation code to check for invalid values. If you
     99      have modified the <filename>extended-properties.xml</filename>
     100      or the <filename>raw-data-types.xml</filename> file and they
     101      contain invalid values, you may not be able to start BASE until
     102      they are fixed. The validation is rather strict and things that may
     103      have worked before (because you were lucky or the because the database
     104      has been forgiving) may no longer work. Here is an overview of the most
     105      important validation rules:
     106    </para>
     107   
     108    <itemizedlist>
     109    <listitem>
     110      <para>
     111      Names and identifiers for extended properties and raw data type
     112      can only contain letters, digits and underscores. They must not
     113      start with a digit.
     114      </para>
     115    </listitem>
     116    <listitem>
     117      <para>
     118      Names of database tables and columns can only contain letters,
     119      digits and underscores. They must not start with a digit.
     120      </para>
     121    </listitem>
     122    <listitem>
     123      <para>
     124      There mustn't be any duplicate tables, columns, properties, etc.
     125      for a given context. For example, no duplicate tables in the
     126      database, no duplicate columns in a table, and no duplicate
     127      properties for a raw data type.
     128      </para>
     129    </listitem>
     130    </itemizedlist>
     131   
    81132  </sect1>
    82133 
  • branches/webservices/doc/src/docbook/developerdoc/plugin_developer.xml

    r3581 r3653  
    7676        <para>
    7777          In the root of your directory, create the build file:
    78           <filename>build.xml</filename>
    79           . Here is an example that will compile your plug-in and put it in a JAR file.
     78          <filename>build.xml</filename>.
     79          Here is an example that will compile your plug-in and put it in a JAR file.
    8080        </para>
    8181        <example id="plugin_developer.organize.build.file">
     
    383383                to be able to function as expected. This method may return null
    384384                or an empty collection. In this case the plug-in permission system
    385                 isn't used and the plug-in always get the same permissions as the
     385                is not used and the plug-in always gets the same permissions as the
    386386                logged in user. If permissions are specified the plug-in should
    387                 list all permissions it require. Permissions that are not listed
     387                list all permissions it requires. Permissions that are not listed
    388388                are denied.
    389389              </para>
     
    518518              <para>
    519519                The <varname>progress</varname> parameter
    520                 can be used by a plug-in to report it's progress back to the core. The
     520                can be used by a plug-in to report its progress back to the core. The
    521521                core will usually send the progress information to the database, which
    522522                allows users to see exactly how the plug-in is progressing from the web
     
    550550              <example id="net.sf.basedb.core.plugin.Plugin.run">
    551551                <title>
    552                   Here is a skeleton that we recommend each plug-in to use in it's
     552                  Here is a skeleton that we recommend each plug-in to use in its
    553553                  implementation of the
    554554                  <methodname>run()</methodname>
     
    881881            <listitem>
    882882              <para>
    883                 Ask the plug-in for parameters that needs to be entered by the user. The
     883                Ask the plug-in for parameters that need to be entered by the user. The
    884884                <classname>GuiContext</classname>
    885885                parameter is one of the contexts returned by the
     
    887887                method. The command is a string telling the plug-in what command was
    888888                executed. There are two predefined commands but as you will see the
    889                 plug-in may define it's own commands. The two predefined commands are
     889                plug-in may define its own commands. The two predefined commands are
    890890                defined in the
    891891                <classname>net.sf.basedb.core.plugin.Request</classname>
     
    15821582          The <methodname>Plugin.init()</methodname> method is called.
    15831583          The <varname>job</varname> parameter contains the job
    1584           configuration paramters. The <varname>configuration</varname> parameter
     1584          configuration parameters. The <varname>configuration</varname> parameter
    15851585          is <constant>null</constant> if the plug-in does not have any
    15861586          configuration parameters.
     
    17061706              object created by your plug-in.
    17071707            </para>
    1708 <programlisting>// Get session control and it's ID (required to post to index.jsp)
     1708<programlisting>// Get session control and its ID (required to post to index.jsp)
    17091709final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
    17101710final String ID = sc.getId();
     
    17781778   try
    17791779   {
     1780      ffp.nextSection();
    17801781      FlatFileParser.LineType result = ffp.parseHeaders();
    1781       return result != FlatFileParser.LineType.UNKNOWN;
     1782      if (result == FlatFileParser.LineType.UNKNOWN)
     1783      {
     1784         return false;
     1785      }
     1786      else
     1787      {
     1788         return isImportable(ffp);
     1789      }
    17821790   }
    17831791   catch (IOException ex)
     
    19371945      <listitem>
    19381946        <para>
    1939         Implement the <methodname>Plugin.getAbout()</methodname> and
    1940         <methodname>Plugin.getMainType()</methodname> methods. See
     1947        Implement the <methodname>Plugin.getAbout()</methodname> method. See
    19411948        <xref linkend="plugin_developer.api.interfaces.plugin" /> for more information.
    19421949        </para>
     
    20542061   ffp.setMinDataColumns(12);
    20552062   return ffp;
     2063}
     2064</programlisting>
     2065        </listitem>
     2066      </varlistentry>
     2067     
     2068      <varlistentry>
     2069        <term>
     2070          <methodsynopsis language="java">
     2071            <modifier>protected</modifier>
     2072            <type>boolean</type>
     2073            <methodname>isImportable</methodname>
     2074            <methodparam>
     2075              <type>FlatFileParser</type>
     2076              <parameter>ffp</parameter>
     2077            </methodparam>
     2078            <exceptionname>IOException</exceptionname>
     2079          </methodsynopsis>
     2080        </term>
     2081        <listitem>
     2082          <para>
     2083          This method is called from the <methodname>isImportable(InputStream)</methodname>
     2084          method, AFTER <methodname>FlatFileParser.nextSection()</methodname> and
     2085          <methodname>FlatFileParser.parseHeaders()</methodname> has been called
     2086          a single time and if the <methodname>parseHeaders</methodname> method didn't
     2087          stop on an unknown line. The default implementation of this method always returns
     2088          TRUE, since obviously some data has been found. A subclass may override this method
     2089          if it wants to do more checks, for example, make that a certain header is present
     2090          with a certain value. It may also continut parsing the file. Here is a code example from
     2091          the <classname>PrintMapFlatFileImporter</classname> which checks if a
     2092          <constant>FormatName</constant> header is present and contains either
     2093          <constant>TAM</constant> or <constant>MwBr</constant>.
     2094          </para>
     2095         
     2096          <programlisting>
     2097/**
     2098   Check that the file is a TAM or MwBr file.
     2099   @return TRUE if a FormatName header is present and contains "TAM" or "MwBr", FALSE
     2100      otherwise
     2101*/
     2102@Override
     2103protected boolean isImportable(FlatFileParser ffp)
     2104{
     2105   String formatName = ffp.getHeader("FormatName");
     2106   return formatName != null &amp;&amp;
     2107      (formatName.contains("TAM") || formatName.contains("MwBr"));
    20562108}
    20572109</programlisting>
     
    24642516        <listitem>
    24652517          <para>
    2466           Set the MIME type of the file that is beeing generated.
     2518          Set the MIME type of the file that is being generated.
    24672519          </para>
    24682520        </listitem>
     
    24822534        <listitem>
    24832535          <para>
    2484           Set a suggested name of the file that is beeing
     2536          Set a suggested name of the file that is being
    24852537          generated.
    24862538          </para>
     
    28662918    <para>
    28672919    Now, the typical <methodname>Plugin.run()</methodname> method loads the specfied bioassay set
    2868     and it's spot data. It may do some filtering and recalculation of the spot
     2920    and its spot data. It may do some filtering and recalculation of the spot
    28692921    intensity value(s). In most cases it will store the result as a child bioassay
    28702922    set with one bioassay for each bioassay in the parent bioassay set.
     
    29382990      <para>
    29392991        This class is an abstract base class. It is a useful
    2940         class for most analysis plug-ins to inherit from. It's main
     2992        class for most analysis plug-ins to inherit from. Its main
    29412993        purpose is to define <classname>PluginParameter</classname>
    29422994        objects that are commonly used in analysis plug-ins. This includes:
     
    29543006      <listitem>
    29553007        <para>
     3008        The optional restriction of which bioassays to use.
     3009        All bioassays in a bioassay set will be used if this
     3010        parameter is empty. This is useful when the plugin only
     3011        should run on a subset of bioassays in a bioassay set:
     3012          <methodname>getSourceBioAssaysParameter()</methodname>,
     3013          <methodname>getSourceBioAssays()</methodname>
     3014        </para>
     3015      </listitem>
     3016      <listitem>
     3017        <para>
    29563018        The name and description of the child bioassay set that
    29573019        is going to be created by the plug-in:
     
    29703032      </itemizedlist>
    29713033     
     3034    </sect2>
     3035   
     3036    <sect2 id="plugin_developer.analyse.filterplugin">
     3037      <title>The AnalysisFilterPlugin interface</title>
     3038     
     3039      <para>
     3040        The <interfacename>net.sf.basedb.core.plugin.AnalysisFilterPlugin</interfacename>
     3041        is a tagging interface with no methods that all analysis plug-ins that only filters
     3042        data should implement. The benefit is that they will be linked from the
     3043        <guibutton>Filter bioassay set</guibutton> button and not just
     3044        the <guibutton>Run analysis</guibutton> button. They will also get
     3045        a different icon in the experiment outline to make filtering
     3046        transformations appear different from other transformations.
     3047      </para>
     3048     
     3049      <para>
     3050        The interface exists purely for making the user interaction better. There is
     3051        no harm in not implementing it since the plug-in will always appear in
     3052        from the <guibutton>Run analysis</guibutton> button. On the other hand,
     3053        it doesn't cost anything to implement the interface since it doesn't
     3054        have any methods.
     3055      </para>
     3056   
    29723057    </sect2>
    29733058
     
    29953080          BASE can authenticate users in two ways. Either it uses the internal
    29963081          authentiction or the external authentication. With internal
    2997           authentication BASE stores logins and passwords in it's own database.
     3082          authentication BASE stores logins and passwords in its own database.
    29983083          With external authentication this is handled by some external
    29993084          application. Even with external authentication it is possible to
     
    31033188          interface. Specify the name of the class in the <property>auth.driver</property>
    31043189          setting in <filename>base.config</filename> and
    3105           it's initialisation parameters in the <property>auth.init</property> setting.
     3190          its initialisation parameters in the <property>auth.init</property> setting.
    31063191        </para>
    31073192       
     
    31303215          <listitem>
    31313216            <para>
    3132             This method is called just after the object has been created with it's argument
     3217            This method is called just after the object has been created with its argument
    31333218            taken from the <property>auth.init</property> setting in your <filename>base.config</filename>
    31343219            file. This method is only called once for an instance of the object. The syntax and meaning of
     
    32073292              <exceptionname>AuthenticationException</exceptionname>:
    32083293              In case there is another problem, such as the authentication service
    3209               beeing down. This exception triggers the use of cached passwords
     3294              being down. This exception triggers the use of cached passwords
    32103295              if caching has been enabled.
    32113296              </para>
     
    32853370    <sect2 id="plugin_developer.other.secondary">
    32863371      <title>Secondary file storage plugins</title>
    3287       <para>
    3288         This documentation is only available in the old format.
    3289         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/plugins/storage/index.html"
    3290           >http://base.thep.lu.se/chrome/site/doc/development/plugins/storage/index.html</ulink>
    3291       </para>
     3372     
     3373      <sect3 id="plugin_developer.other.secondary.vsprimary">
     3374        <title>Primary vs. secondary storage</title>
     3375        <para>
     3376          BASE has support for storing files in two locations, the primary storage and
     3377          the secondary storage. The primary storage is always disk-based and must be
     3378          accessible by the BASE server as a path on the file system. The path to the
     3379          primary storage is configured by the <varname>userfiles</varname> setting in the
     3380          <filename>base.config</filename> file. The primary storage is internal to
     3381          the core. Client applications don't get access to read or manipulate the
     3382          files directly from the file system.
     3383        </para>
     3384       
     3385        <para>
     3386          The secondary storage can be anything that can store files. It could, for
     3387          example, be another directory, a remote FTP server, or a tape based archiving
     3388          system. A file located in the secondary storage is not accessible by the
     3389          core, client applications or plug-ins. The secondary storage can only be accessed
     3390          by the secondary storage controller. The core (and client) applications uses
     3391          flags on the file items to handle the interaction with the secondary storage.
     3392        </para>
     3393       
     3394        <para>
     3395          Each file has an <property>action</property> attribute which default's to
     3396          <constant>File.Action.NOTHING</constant>. It can take two other values:
     3397        </para>
     3398       
     3399        <orderedlist>
     3400        <listitem>
     3401          <para>
     3402          <constant>File.Action.MOVE_TO_SECONDARY</constant>
     3403          </para>
     3404        </listitem>
     3405        <listitem>
     3406          <para>
     3407          <constant>File.Action.MOVE_TO_PRIMARY</constant>
     3408          </para>
     3409        </listitem>
     3410        </orderedlist>
     3411       
     3412        <para>
     3413          All files with the action attribute set to <constant>MOVE_TO_SECONDARY</constant>
     3414          should be moved to the secondary storage by the controller, and all files
     3415          with the action attribute set to <constant>MOVE_TO_PRIMARY</constant> should be
     3416          brought back to primary storage.
     3417        </para>
     3418       
     3419        <para>
     3420          The moving of files between primary and secondary storage doesn't happen
     3421          immediately. It is up to the server administrator to configure how often and
     3422          at what times the controller should check for files that should be moved.
     3423          This is configured by the <varname>secondary.storage.interval</varname>
     3424          and <varname>secondary.storage.time</varname> settings in the
     3425          <filename>base.config</filename> file.       
     3426        </para>
     3427      </sect3>
     3428     
     3429      <sect3 id="plugin_developer.other.secondary.interface">
     3430        <title>The SecondaryStorageController interface</title>
     3431       
     3432        <para>
     3433          All you have to do to create a secondary storage controller is to
     3434          create a class that implements the
     3435          <interfacename>net.sf.basedb.core.SecondaryStorageController</interfacename>
     3436          interface. In your <filename>base.config</filename> file you then specify the
     3437          class name in the <varname>secondary.storage.driver</varname> setting and its
     3438          initialisation parameters in the <varname>secondary.storage.init</varname> setting.
     3439        </para>
     3440
     3441        <para>
     3442          Your class must have a public no-argument constructor.
     3443          The BASE application will create only one instance of the class for
     3444          lifetime of the BASE server. Here are the methods that you must implement:
     3445        </para>
     3446       
     3447        <variablelist>
     3448        <varlistentry>
     3449          <term>
     3450          <methodsynopsis language="java">
     3451            <modifier>public</modifier>
     3452            <void />
     3453            <methodname>init</methodname>
     3454            <methodparam>
     3455              <type>String</type>
     3456              <parameter>settings</parameter>
     3457            </methodparam>
     3458          </methodsynopsis>
     3459          </term>
     3460          <listitem>
     3461            <para>
     3462            This method is called just after the object has been created with its argument
     3463            taken from the <varname>secondary.storage.init</varname> setting in your
     3464            <filename>base.config</filename> file. This method is only called once for
     3465            an object.
     3466            </para>
     3467          </listitem>
     3468        </varlistentry>
     3469        <varlistentry>
     3470          <term>
     3471          <methodsynopsis language="java">
     3472            <modifier>public</modifier>
     3473            <void />
     3474            <methodname>run</methodname>
     3475          </methodsynopsis>
     3476          </term>
     3477          <listitem>
     3478            <para>
     3479            This method is called whenever the core thinks it is time to do some
     3480            management of the secondary storage. How often the <methodname>run()</methodname>
     3481            method is called is controlled by the <varname>secondary.storage.interval</varname>
     3482            and <varname>secondary.storage.time</varname> settings in the
     3483            <filename>base.config</filename> file.
     3484            When this method is called the controller should:
     3485            </para>
     3486           
     3487            <itemizedlist>
     3488            <listitem>
     3489              <para>
     3490              Move all files which has <constant>action=MOVE_TO_SECONDARY</constant> to
     3491              the secondary storage. When the file has been moved call
     3492              <methodname>File.setLocation(Location.SECONDARY)</methodname> to tell the
     3493              core that the file is now in the secondary storage. You should also call
     3494              <methodname>File.setAction(File.Action.NOTHING)</methodname> to reset the
     3495              action attribute.
     3496              </para>
     3497            </listitem>
     3498           
     3499            <listitem>
     3500              <para>
     3501              Restore all files which has <constant>action=MOVE_TO_PRIMARY</constant>.
     3502              The core will set the location attribute automatically, but you should
     3503              call <methodname>File.setAction(File.Action.NOTHING)</methodname> to reset
     3504              the action attribute.
     3505              </para>
     3506            </listitem>
     3507           
     3508            <listitem>
     3509              <para>
     3510              Delete all files from the secondary storage that are not present
     3511              in the database with <constant>location=Location.SECONDARY</constant>.
     3512              This includes files which has been deleted and files that have been
     3513              moved offline or re-uploaded.
     3514              </para>
     3515            </listitem>
     3516           
     3517            </itemizedlist>
     3518           
     3519            <para>
     3520              As a final act the method should send a message to each user owning
     3521              files that has been moved from one location to the other. The message
     3522              should include a list of files that has been moved to the secondary
     3523              storage and a list of files moved from the secondary storage and a
     3524              list of files that has been deleted due to some of the reasons above.
     3525            </para>
     3526          </listitem>
     3527        </varlistentry>       
     3528       
     3529        <varlistentry>
     3530          <term>
     3531          <methodsynopsis language="java">
     3532            <modifier>public</modifier>
     3533            <void />
     3534            <methodname>close()</methodname>
     3535          </methodsynopsis>
     3536          </term>
     3537          <listitem>
     3538            <para>
     3539            This method is called when the server is closing down. After this the object
     3540            is never used again.
     3541            </para>
     3542          </listitem>
     3543        </varlistentry>
     3544        </variablelist>
     3545      </sect3>
     3546     
     3547      <sect3 id="plugin_developer.other.secondary.settings">
     3548        <title>Configuration settings</title>
     3549       
     3550        <para>
     3551        The configuration settings for the secondary storage controller is located in the
     3552        <filename>base.config</filename> file. Here is an overview of the settings.
     3553        For more information read <xref linkend="appendix.base.config" />.
     3554        </para>
     3555       
     3556        <variablelist>
     3557        <varlistentry>
     3558          <term><property>secondary.storage.driver</property></term>
     3559          <listitem>
     3560            <para>
     3561            The class name of the secondary storage plug-in.
     3562            </para>
     3563          </listitem>
     3564        </varlistentry>
     3565        <varlistentry>
     3566          <term><property>secondary.storage.init</property></term>
     3567          <listitem>
     3568            <para>
     3569             Initialisation parameters sent to the plug-in by calling the
     3570             <methodname>init()</methodname> method.
     3571            </para>
     3572          </listitem>
     3573        </varlistentry>
     3574        <varlistentry>
     3575          <term><property>secondary.storage.interval</property></term>
     3576          <listitem>
     3577            <para>
     3578             Interval in seconds between each execution of the secondary storage
     3579             controller plug-in.
     3580            </para>
     3581          </listitem>
     3582        </varlistentry>
     3583        <varlistentry>
     3584          <term><property>secondary.storage.time</property></term>
     3585          <listitem>
     3586            <para>
     3587              Time points during the day when the secondary storage controller plugin
     3588              should be executed.
     3589            </para>
     3590          </listitem>
     3591        </varlistentry>
     3592        </variablelist>
     3593      </sect3>
    32923594    </sect2>
    32933595   
     
    33003602        BASE distribution comes with support for ZIP files
    33013603        (<classname>net.sf.basedb.plugins.ZipFileUnpacker</classname>)
    3302         and TAR files (<classname>net.sf.basedb.plugins.ZipFileUnpacker</classname>).
     3604        and TAR files (<classname>net.sf.basedb.plugins.TarFileUnpacker</classname>).
    33033605      </para>
    33043606      <para>
     
    34963798     
    34973799    </sect2>
     3800   
     3801    <sect2 id="plugin_developer.other.packer">
     3802      <title>File packer plug-ins</title>
     3803   
     3804      <para>
     3805        BASE has support for compressing and downloading a set of selected files and/or
     3806        directories. This functionality is provided by a plug-in, the
     3807        <classname>PackedFileExporter</classname>. This plug-in doesn't do the actual
     3808        packing itself. This is delegated to classes implementing the
     3809        <interfacename>net.sf.basedb.util.zip.FilePacker</interfacename> interface.
     3810      </para>
     3811     
     3812      <para>
     3813        BASE ships with a number of packing methods, including ZIP and TAR. To
     3814        add support for other methods you have to provide an implementation
     3815        of the <interfacename>FilePacker</interfacename>
     3816        interface. Then, create a new configuration for the <classname>PackerFileExporter</classname>
     3817        and enter the name of your class in the configuration wizard.
     3818      </para>
     3819     
     3820      <para>
     3821        The <interfacename>FilePacker</interfacename> interface is not a regular
     3822        plug-in interface (ie. it is not a subinterface to
     3823        <interfacename>Plugin</interfacename>). This means that you don't have to
     3824        mess with configuration or job parameters. Another difference is that your
     3825        class must be installed in Tomcat's classpath (ie. in one of the
     3826        <filename>WEB-INF/classes</filename> or <filename>WEB-INF/lib</filename>
     3827        folders).
     3828      </para>
     3829     
     3830      <variablelist>
     3831        <title>Methods in the <interfacename>FilePacker</interfacename> interface</title>
     3832        <varlistentry>
     3833          <term>
     3834            <methodsynopsis language="java">
     3835              <modifier>public</modifier>
     3836              <type>String</type>
     3837              <methodname>getDescription</methodname>
     3838            </methodsynopsis>
     3839          </term>
     3840          <listitem>
     3841            <para>
     3842            Return a short description the file format that is suitable for use
     3843            in dropdown lists in client applications. For example:
     3844            <constant>Zip-archive (.zip)</constant> or <constant>TAR-archive (.tar)</constant>.
     3845            </para>
     3846          </listitem>
     3847        </varlistentry>
     3848        <varlistentry>
     3849          <term>
     3850            <methodsynopsis language="java">
     3851              <modifier>public</modifier>
     3852              <type>String</type>
     3853              <methodname>getFileExtension</methodname>
     3854            </methodsynopsis>
     3855          </term>
     3856          <listitem>
     3857            <para>
     3858            Return the default file extension of the packed format. The returned
     3859            value should not include the dot. For example:
     3860            <constant>zip</constant> or <constant>tar</constant>.
     3861            </para>
     3862          </listitem>
     3863        </varlistentry>
     3864        <varlistentry>
     3865          <term>
     3866            <methodsynopsis language="java">
     3867              <modifier>public</modifier>
     3868              <type>String</type>
     3869              <methodname>getMimeType</methodname>
     3870            </methodsynopsis>
     3871          </term>
     3872          <listitem>
     3873            <para>
     3874            Return the standard MIME type of the packed file format.
     3875            For example:
     3876            <constant>application/zip</constant> or <constant>application/x-tar</constant>.
     3877            </para>
     3878          </listitem>
     3879        </varlistentry>
     3880        <varlistentry>
     3881          <term>
     3882            <methodsynopsis language="java">
     3883              <modifier>public</modifier>
     3884              <void />
     3885              <methodname>setOutputStream</methodname>
     3886              <methodparam>
     3887                <type>OutputStream</type>
     3888                <parameter>out</parameter>
     3889              </methodparam>
     3890              <exceptionname>IOException</exceptionname>
     3891            </methodsynopsis>
     3892          </term>
     3893          <listitem>
     3894            <para>
     3895            Sets the outputstream that the packer should write the packed
     3896            files to.
     3897            </para>
     3898          </listitem>
     3899        </varlistentry>
     3900        <varlistentry>
     3901          <term>
     3902            <methodsynopsis language="java">
     3903              <modifier>public</modifier>
     3904              <void />
     3905              <methodname>pack</methodname>
     3906              <methodparam>
     3907                <type>String</type>
     3908                <parameter>entryName</parameter>
     3909              </methodparam>
     3910              <methodparam>
     3911                <type>InputStream</type>
     3912                <parameter>in</parameter>
     3913              </methodparam>
     3914              <methodparam>
     3915                <type>long</type>
     3916                <parameter>size</parameter>
     3917              </methodparam>
     3918              <methodparam>
     3919                <type>long</type>
     3920                <parameter>lastModified</parameter>
     3921              </methodparam>
     3922              <exceptionname>IOException</exceptionname>
     3923            </methodsynopsis>
     3924          </term>
     3925          <listitem>
     3926            <para>
     3927            Add another file or directory to the packed file. The
     3928            <parameter>entryName</parameter> is the name of the new entry, including
     3929            path information. The <parameter>in</parameter> is the stream to read
     3930            the file data from. If <parameter>in</parameter> is <constant>null</constant>
     3931            then the entry denotes a directory. The <parameter>size</parameter> parameter
     3932            gives the size in bytes of the file (zero for empty files or directories).
     3933            The <parameter>lastModified</parameter>
     3934            is that time the file was last modified or 0 if not known.
     3935            </para>
     3936          </listitem>
     3937        </varlistentry>
     3938        <varlistentry>
     3939          <term>
     3940            <methodsynopsis language="java">
     3941              <modifier>public</modifier>
     3942              <void />
     3943              <methodname>close</methodname>
     3944              <exceptionname>IOException</exceptionname>
     3945            </methodsynopsis>
     3946          </term>
     3947          <listitem>
     3948            <para>
     3949            Finish the packing. The packer should release any resources, flush
     3950            all data and close all output streams, including the <varname>out</varname> stream
     3951            set in the <methodname>setOutputStream</methodname> method.
     3952            </para>
     3953          </listitem>
     3954        </varlistentry>
     3955       
     3956      </variablelist>
     3957     
     3958    </sect2>
    34983959  </sect1>
    34993960 
     
    35013962    <title>Example plug-ins (with download)</title>
    35023963    <para>
    3503       <para>
    3504         This documentation is only available in the old format.
    3505         See <ulink url="http://base.thep.lu.se/chrome/site/doc/development/index.html#plugins"
    3506           >http://base.thep.lu.se/chrome/site/doc/development/index.html#plugins</ulink>
    3507       </para>
     3964      We have created some example plug-ins which demonstrates how to
     3965      use the plug-in system and how to create an interactive plug-in that
     3966      can ask a user for one or more parameters.
     3967   
     3968      <ulink url="../../../download/exampleplugins.tar.gz">Download</ulink>
     3969      a tar file with the source and compiled code. It contains the followin
     3970      plug-ins:
    35083971    </para>
     3972   
     3973    <variablelist>
     3974    <varlistentry>
     3975      <term>ExampleImporter</term>
     3976      <listitem>
     3977        <para>
     3978        An import plug-in that pretends to import samples. It will ask for a file
     3979        and if existing samples should be updated or not, but doesn't actually
     3980        import anything.
     3981        </para>
     3982      </listitem>
     3983    </varlistentry>
     3984
     3985    <varlistentry>
     3986      <term>ExampleAnalyzer</term>
     3987      <listitem>
     3988        <para>
     3989        An analysis plug-in that asks for a multiplication factor and a cut-off value.
     3990        It will create a child bioassay set by multiplying the original intensities
     3991        with the given factor and filter out those with original intensities less
     3992        than the cut-off. It works for any number of channels and raw data types
     3993        </para>
     3994      </listitem>
     3995    </varlistentry>
     3996    </variablelist>
     3997
    35093998  </sect1>
    35103999</chapter>
  • branches/webservices/doc/src/docbook/userdoc/annotations.xml

    r3533 r3653  
    692692    </sect2>
    693693   
     694    <sect2 id="annotations.massimport">
     695      <title>Mass annotation import plug-in</title>
     696     
     697      <para>
     698        BASE includes a plug-in for importing annotations to multiple items
     699        in one go. The plug-in read annotation values from a simple column-based
     700        text file. Ususally, a tab is used as the delimiter between columns.
     701        The first row should contain the column headers. One column should contain
     702        the name or the external ID of the item. The rest of the columns can each be
     703        mapped to an annotation type and contains the annotation values. If a column
     704        header exactly match the name of an annotation type, the plug-in will automatically
     705        create the mapping, otherwise you must do it manually. You don't have to map
     706        all columns if you don't want to.
     707      </para>
     708     
     709      <para>
     710        Each column can only contain a single annotation value for each row.
     711        If you have annotation types that accept multiple values you can map
     712        two or more columns to the same annotation type, or you can add an
     713        extra row only giving the name and the extra annotation value.
     714        Here is a simple example of a valid file with comma as column separator:
     715      </para>
     716     
     717      <programlisting>
     718# 'Time' and 'Age' are integer types
     719# 'Subtype' is a string enumeration
     720# 'Comment' is a text type that accept multiple values
     721Name,Time (hours),Age (years),Subtype,Comment
     722Sample #1,0,0,alfa,Very good
     723Sample #2,24,0,beta,Not so bad
     724Sample #2,,,,Yet another comment
     725</programlisting>
     726     
     727      <para>
     728        The plug-in can be used with or without a configuration. The configuration
     729        keeps the regular expressions and other settings used to parse the file. If
     730        you often import annotations from the same file format, we recommend that
     731        you use a configuration. The mapping from file columns to annotation types
     732        is not part of the configuration, it must be done each time the plug-in is used.
     733      </para>
     734     
     735      <para>
     736        The plug-in can be used from the list view of all annotatable items.
     737        Using the plug-in is a three-step wizard:
     738      </para>
     739     
     740      <orderedlist>
     741      <listitem>
     742        <para>
     743        Select a file to import from and the regular expressions and other
     744        settings used to parse the file. In this step you also select the column
     745        that contains the name or external ID the items. If a configuration is used
     746        all settings on this page, except the file to import from, already has values.
     747        </para>
     748      </listitem>
     749     
     750      <listitem>
     751        <para>
     752        The plug-in will start parsing the file until it finds the column headers.
     753        You are asked to select an annotation type for each column.
     754        </para>
     755      </listitem>
     756     
     757      <listitem>
     758        <para>
     759        Set error handling options and some other import options.
     760        </para>
     761      </listitem>
     762     
     763      </orderedlist>
     764     
     765    </sect2>
     766   
    694767  </sect1>
    695768
  • branches/webservices/doc/src/docbook/userdoc/file_system.xml

    r3581 r3653  
    685685        </para>
    686686      </sect3>
     687      <sect3 id="file_system.handling.actions.zippeddownload">
     688        <title>Download/compress multiple files</title>
     689       
     690        <para>
     691        You can download multiple files/directories at the same time. First,
     692        from the file browser, select one or more files/directories. Then, click
     693        on the &gbExport; button. Select the <userinput>Packed file exporter</userinput>
     694        plug-in and choose one of the file formats below it. On the &gbNext;
     695        page you can specify other options for the download:
     696        </para>
     697       
     698        <itemizedlist>
     699        <listitem>
     700          <para>
     701            <guilabel>Save as</guilabel>: The path to a file on the BASE file system
     702            where the selected files and directories should be packed. Leave this
     703            field empty to download the files to your own computer.
     704          </para>
     705        </listitem>
     706        <listitem>
     707          <para>
     708            <guilabel>Overwrite</guilabel>: If you are saving to the BASE file system
     709            you may select if it is allowed to overwrite an existing file or not.
     710          </para>
     711        </listitem>
     712        <listitem>
     713          <para>
     714            <guilabel>Remove files/directories</guilabel>: If you select this option
     715            the selected files and directories will be marked as removed. You must still
     716            go to the <guilabel>Trashcan</guilabel> and remove the items permanently.
     717          </para>
     718        </listitem>
     719        </itemizedlist>
     720       
     721      </sect3>
    687722    </sect2>
    688723    <sect2 id="file_system.handling.directories">
  • branches/webservices/doc/src/docbook/userdoc/jobs.xml

    • Property svn:keywords set to Id Date
  • branches/webservices/doc/src/docbook/userdoc/reporters.xml

    r3533 r3653  
    322322     
    323323      <para>
    324         Reporters which has been referenced to from raw data, array
     324        Reporters which has been referenced to from reporter lists, raw data, array
    325325        designs, plates or any other item cannot be deleted.
    326326      </para>
     327     
     328      <sect3 id="reporter.delete.batch">
     329        <title>Batch deletion</title>
     330        <para>
     331          A common problem is to delete reporters that has been accidentaly
     332          created. The regular web interface is usually no good since it
     333          only allows you to select at most 99 reporters at a time. To solve
     334          this problem the reporter import plug-in can be used in delete mode.
     335          You can use the same file as you used when importing. Just select
     336          the <userinput>delete</userinput> option for the <guilabel>mode</guilabel>
     337          parameter in the configuration wizard and continue as usual.
     338          If the plug-in is used in delete mode from a reporter list it will
     339          only remove the reporters from the reporter list. The reporters are not
     340          deleted from the database.
     341        </para>
     342       
     343        <note>
     344          <para>
     345          It may be a bit confusing to delete things from an import plug-in. But
     346          since plug-ins can only belong to one category and we wanted to re-use
     347          existing file format definitions this was our only option.
     348          </para>
     349        </note>
     350      </sect3>
     351     
    327352    </sect2>
    328353
  • branches/webservices/lib/docbook/module-fop/lib/batik.LICENSE.txt

    • Property svn:eol-style set to native
    • Property svn:keywords set to Id Date
  • branches/webservices/src/clients/migrate/net/sf/basedb/clients/migrate/FileTransfer.java

    r3533 r3653  
    154154        fis.close();
    155155        return md5.toString(16);
     156      }
     157      else
     158      {
     159        log.warn("BASE 1 file doesn't exists: " + file.toString());
    156160      }
    157161    }
  • branches/webservices/src/clients/migrate/net/sf/basedb/clients/migrate/Migrater.java

    r3533 r3653  
    3838import java.sql.SQLException;
    3939import java.util.HashMap;
     40import java.util.HashSet;
    4041import java.util.Properties;
     42import java.util.Set;
    4143import java.util.regex.Matcher;
    4244import java.util.regex.Pattern;
     
    5254public class Migrater extends Manager
    5355{
     56 
     57  public static Set<String> supportedBase1Versions = new HashSet<String>();
     58  static
     59  {
     60    supportedBase1Versions.add("1.2.20");
     61    supportedBase1Versions.add("1.2.21");
     62  }
     63 
    5464  /**
    5565  Holds properties defined in migrate.properties
     
    431441      String schemaVersion = rs.getString(2);
    432442      ps.close();
    433       if (!schemaVersion.equals("1.2.20"))
     443      if (!supportedBase1Versions.contains(schemaVersion))
    434444      {
    435445        log.error("Migration cannot proceed due to incompatible schema version. Your schema version is "
    436             + schemaVersion + " and this migration needs 1.2.20");
     446            + schemaVersion + " and this migration needs one of: " + supportedBase1Versions);
    437447        stop();
    438448      }     
  • branches/webservices/src/clients/migrate/net/sf/basedb/clients/migrate/RawBioAssayDataTransfer.java

    r3533 r3653  
    3636
    3737/**
    38 This class provides methods for transferring RawBioAssay and RawBioAssayData
    39 from base 1 to BASE 2. Base 1 files are located in /userfiles/rawdata/
    40 
    41 @author Gregory, Martin
    42 @version 2.0
    43 @base.modified $Date$
     38  This class provides methods for transferring RawBioAssay and RawBioAssayData
     39  from base 1 to BASE 2. Base 1 files are located in /userfiles/rawdata/
     40 
     41  @author Gregory, Martin
     42  @version 2.0
     43  @base.modified $Date$
    4444*/
    4545
    46 public class RawBioAssayDataTransfer extends CommonItemTransfer
     46public class RawBioAssayDataTransfer
     47  extends CommonItemTransfer
    4748{
    4849  /**
     
    172173  values from and size.
    173174 
    174   @param ps <code>PreparedStatement</code>
    175   @param batcher RawDataBatcher used in this transfer.
     175  @param rawBioAssay The raw bio assay to transfer data to
     176  @param batcher RawDataBatcher used in this transfer
    176177  @param hasArrayDesign (Currently not used)
     178  @param base1RawBioAssayId The ID of the raw bioassay in the BASE 1.2 installation
    177179  @see Transfer#prepareStatementFromFile(String)
    178180   */
  • branches/webservices/src/clients/migrate/net/sf/basedb/clients/migrate/ReporterTransfer.java

    r3533 r3653  
    7171 
    7272  /**
     73    Maps BASE 1 reporters that are considered duplicate by BASE 2 after
     74    whitespace has been trimmed from the external ID. Only used temporary until the
     75    reporterMap is generated. Map contain BASE 1 ID --> Base 1 ID where the value
     76    is the "real" reporter that is migrated to BASE 2.
     77  */
     78  private Map<Integer, Integer> duplicates = null;
     79 
     80  /**
    7381    Used for inserting reporter into Base 2.
    7482  */
     
    97105   
    98106    int count = getInt("countReporters");
    99     startProgress(count*2, "Reporters"); // First pass creates reporters, second one reads in the new ID:s
     107    // First pass creates reporters...
     108    startProgress(count, "Reporters");
    100109    PreparedStatement ps = QUICK_TRANSFER ? prepareStatementFromFile("selectMinimumReporters")
    101110        : prepareStatementFromFile("selectReporters");
    102111
    103112    externalIdMap = new HashMap<String, Integer>(count);
    104     DbControl dc = newDbControl();
     113    duplicates = new HashMap<Integer, Integer>();
     114    DbControl dc = null;
    105115    try
    106116    {
     117      dc = newDbControl();
    107118      batcher = ReporterBatcher.getNew(dc);
    108119      batcher.setBatchSize(getBatchSize());
     
    110121      batcher.close();
    111122      dc.commit();
    112      
     123    }
     124    finally
     125    {
     126      if (dc != null) dc.close();
     127      progress.stop();
     128    }
     129   
     130    // ... second pass reads in the new ID:s
     131    progress = null;
     132    startProgress(count, "Mapping reporter ID:s");
     133    try
     134    {
    113135      reporterMap = new HashMap<Integer, ReporterData>(count);
     136      dc = newDbControl();
    114137      log.info("Mapping reporters in BASE 2...");
    115       mapReporters(0, getBatchSize());
     138      int start = 0;
     139      int batchSize = getBatchSize();
     140
     141      DataQuery<ReporterData> query = Reporter.getQuery();
     142      query.order(Orders.asc(Hql.property("id")));
     143      query.setMaxResults(batchSize);
     144      while (start < count)
     145      {
     146        query.setFirstResult(start);
     147        cleanUpMemory();
     148        mapMigratedReporters(dc, query);
     149        start += batchSize;
     150      }
    116151      cleanUpMemory();
     152      mapDuplicateReporters();
    117153    }
    118154    finally
     
    120156      if (dc != null) dc.close();
    121157      externalIdMap.clear();
     158      duplicates.clear();
    122159      progress.stop();
    123160    }
     
    152189        rowCount++;
    153190        ReporterData item = createDataItem(rs);
    154         batcher.insert(item);
     191        if (item != null) batcher.insert(item);
    155192        progress.increase();
    156193        if (log.isDebugEnabled())
     
    179216  }
    180217
    181   private void mapReporters(int from, int size)
    182   {
    183     cleanUpMemory();
    184     int rowCount = 0;
    185     DbControl dc = newDbControl();
     218  private void mapMigratedReporters(DbControl dc, DataQuery<ReporterData> query)
     219  {
    186220    DataResultIterator<ReporterData> result = null;
    187221    try
    188222    {
    189       DataQuery<ReporterData> query = Reporter.getQuery();
    190       query.order(Orders.asc(Hql.property("id")));
    191       query.setFirstResult(from);
    192       query.setMaxResults(size);
    193223      result = query.iterate(dc);
    194224      while (result.hasNext())
    195225      {
    196226        ReporterData reporter = result.next();
    197         reporterMap.put(externalIdMap.get(reporter.getExternalId()), new ReporterProxy(reporter));
    198         rowCount++;
     227        Integer base1Id = externalIdMap.get(reporter.getExternalId());
     228        reporterMap.put(base1Id, new ReporterProxy(reporter));
    199229        progress.increase();
    200230        if (log.isDebugEnabled())
    201231        {
    202           log.debug("Reporter: " + reporter.getExternalId() + " has been mapped");
     232          log.debug("Reporter: " + reporter.getExternalId() +
     233            " has been mapped to BASE 1 ID="+base1Id);
    203234        }
    204235      }
     
    207238    {
    208239      if (result != null) result.close();
    209       if (dc != null) dc.close();
    210     }
    211     if (rowCount == size)
    212     {
    213       mapReporters(from+size, size);
    214     }
    215   }
    216 
     240    }
     241  }
     242
     243  private void mapDuplicateReporters()
     244  {
     245    // The map contains base1Id of duplicate -> base1Id of transfered reporter
     246    for (Map.Entry<Integer, Integer> entry : duplicates.entrySet())
     247    {
     248      Integer duplicateId = entry.getKey();
     249      Integer migratedId = entry.getValue();
     250      ReporterData migratedReporter = reporterMap.get(migratedId);
     251      reporterMap.put(duplicateId, migratedReporter);
     252      progress.increase();
     253      if (log.isDebugEnabled())
     254      {
     255        log.debug("Reporter: " + migratedReporter.getExternalId() +
     256          " has been mapped to BASE 1 ID=" + duplicateId);
     257      }
     258    }
     259  }
     260 
     261 
    217262
    218263  /**
     
    221266 
    222267  @param rs <code>ResultSet</code> containing the data for this item.
    223   @return <code>ReporterData</code>
     268  @return <code>ReporterData</code> or null if another reporter with same ID has already been created
    224269  @throws BaseException
    225270  @throws SQLException If current ResultSet position is invalid or number
     
    230275  {
    231276    // Populate a new ReporterData object   
    232     String externalId = rs.getString(2);
    233     ReporterData rd = Reporter.getNew(externalId);
    234     if (log.isDebugEnabled())
    235     {
    236       log.debug("Transfering Reporter BASE1 id(" + rs.getInt(1) + ")\texternal Id(" + externalId + ")");
    237     }
    238     externalIdMap.put(externalId, rs.getInt(1));
    239     if (!QUICK_TRANSFER)
    240     {
    241       String name = rs.getString(3);
    242       if (name == null || "".equals(name)) name = externalId;
    243       rd.setName(name);
    244       rd.setSymbol(rs.getString(4));
    245       int columnIndex = 5;
    246       for (String property : stringProperties)
    247       {
    248         rd.setExtended(property, rs.getString(columnIndex));
    249         columnIndex++;
    250       }
    251       // Set integer properties, integer properties should be listed
    252       // last(after the string properties) in the select statement
    253       String[] intProperties = { "length" };
    254       for (String property : intProperties)
    255       {
    256         rd.setExtended(property, rs.getInt(columnIndex));
    257         columnIndex++;
    258       }
    259     }   
     277    String externalId = rs.getString(2).trim();
     278    int base1Id = rs.getInt(1);
     279    ReporterData rd = null;
     280    if (externalIdMap.containsKey(externalId))
     281    {
     282      Integer migratedBase1Id = externalIdMap.get(externalId);
     283      log.warn("Duplicate reporter found in BASE 1 after trimming whitespace: id=" +
     284        base1Id + "; externald ID=" + externalId + "; Merging this reporter with reporter id="+
     285        migratedBase1Id);
     286      duplicates.put(base1Id, migratedBase1Id);
     287    }
     288    else
     289    {
     290      externalIdMap.put(externalId, base1Id);
     291      if (log.isDebugEnabled())
     292      {
     293        log.debug("Transfering Reporter BASE1 id(" + base1Id + ")\texternal Id(" + externalId + ")");
     294      }
     295      rd = Reporter.getNew(externalId);
     296      if (!QUICK_TRANSFER)
     297      {
     298        String name = rs.getString(3);
     299        if (name == null || "".equals(name)) name = externalId;
     300        rd.setName(name);
     301        rd.setSymbol(rs.getString(4));
     302        int columnIndex = 5;
     303        for (String property : stringProperties)
     304        {
     305          rd.setExtended(property, rs.getString(columnIndex));
     306          columnIndex++;
     307        }
     308        // Set integer properties, integer properties should be listed
     309        // last(after the string properties) in the select statement
     310        String[] intProperties = { "length" };
     311        for (String property : intProperties)
     312        {
     313          rd.setExtended(property, rs.getInt(columnIndex));
     314          columnIndex++;
     315        }
     316      }
     317    }
    260318    return rd;
    261319  }
  • branches/webservices/src/clients/migrate/net/sf/basedb/clients/migrate/SampleTissueTransfer.java

    r3533 r3653  
    7272  Recursive run over a SQL query defined by a prepared statement and LIMIT
    7373  values from and size. If this method is called directly from a child
    74   transfer, remember to call {@link #startProgress(int)} before you call
     74  transfer, remember to call {@link #startProgress(int, String)} before you call
    7575  this method
    7676 
  • branches/webservices/src/clients/migrate/net/sf/basedb/clients/migrate/Transfer.java

    r3533 r3653  
    269269  Recursive run over a SQL query defined by a prepared statement and LIMIT
    270270  values from and size. If this method is called directly from a child
    271   transfer, remember to call {@link #startProgress(int)} before you call
     271  transfer, remember to call {@link #startProgress(int, String)} before you call
    272272  this method
    273273 
     
    339339  Run over a SQL query defined by a prepared statement. If this method is
    340340  called directly from a child transfer, remember to call
    341   {@link #startProgress(int)} before you call this method
     341  {@link #startProgress(int, String)} before you call this method
    342342 
    343343  @param ps <code>PreparedStatement</code>
  • branches/webservices/src/clients/migrate/net/sf/basedb/clients/migrate/WizzzardTransfer.java

    r3533 r3653  
    5959public class WizzzardTransfer extends CommonItemTransfer
    6060{
     61  private static final org.apache.log4j.Logger log = org.apache.log4j.Logger.getLogger("net.sf.basedb.clients.migrate.WizzzardTransfer");
     62
    6163  /**
    6264  @param userT A finished {@link UserTransfer}
    6365  @param groupT A finished {@link GroupTransfer}
    6466   */
    65   private static final org.apache.log4j.Logger log = org.apache.log4j.Logger.getLogger("net.sf.basedb.clients.migrate.WizzzardTransfer");
    66  
    6767  WizzzardTransfer(UserTransfer userT, GroupTransfer groupT)
    6868  {
  • branches/webservices/src/core/common-queries.xml

    r3581 r3653  
    15401540    </description>
    15411541  </query>
     1542
     1543  <query id="GET_PLUGINCONFIGURATION_FOR_PLUGIN_WITH_NAME" type="HQL">
     1544    <sql>
     1545      SELECT pc
     1546      FROM PluginConfigurationData pc
     1547      WHERE pc.pluginDefinition.className = :className
     1548      AND pc.name = :name
     1549    </sql>
     1550    <description>
     1551      Load a plugin configuration for a given plug-in and with a given name
     1552    </description>
     1553  </query>
     1554
    15421555
    15431556  <query id="GET_EXPERIMENTS_FOR_RAWBIOASSAY" type="HQL">
     
    26882701  </query>
    26892702 
     2703  <query id="UPDATE_PROPERTY_FILTER" type="SQL">
     2704    <sql>
     2705      UPDATE [PropertyFilters]
     2706      SET [property] = :newProperty
     2707      WHERE [property] = :oldProperty
     2708    </sql>
     2709    <description>
     2710      An SQL query that changes the property for all PropertyFilters
     2711      with a given value.
     2712    </description>
     2713  </query>
    26902714 
    26912715
  • branches/webservices/src/core/net/sf/basedb/core/AnnotationType.java

    r3533 r3653  
    10941094      if (pv == null || !pv.getValues().contains(value))
    10951095      {
    1096         throw new InvalidDataException("Value '"+value+"' is not among the list of allowed values: "+(pv == null ? "" : pv.getValues()));
     1096        throw new DisallowedValueException("Value '"+value+"' is not among the list of allowed values " +
     1097          "for annotation type: "+getName());
    10971098      }
    10981099    }
  • branches/webservices/src/core/net/sf/basedb/core/Application.java

    r3533 r3653  
    136136 
    137137  /**
     138    Allow automatic unload of plug-in JAR files or not.
     139  */
     140  private static boolean autoUnloadPlugins;
     141 
     142  /**
    138143    The host name of the server running BASE.
    139144  */
     
    388393      log.info("db.batch-size = " + Config.getString("db.batch-size"));
    389394 
     395      autoUnloadPlugins = Config.getBoolean("plugins.autounload");
     396      log.info("plugins.autounload = " + autoUnloadPlugins);
     397     
    390398      // Create a cache for SessionControl objects
    391399      sessionCache = Collections.synchronizedMap(new HashMap<String,SessionControl>());
    392400     
    393401      // Initialise other utility classes
     402      HibernateUtil.init1();
    394403      ExtendedProperties.init();
    395404      RawDataTypes.init();
    396405      RawDataUtil.init();
    397       HibernateUtil.init();
     406      HibernateUtil.init2();
    398407      QueryRuntimeFilterFactory.init();
    399408      PredefinedQuery.init();
     
    695704
    696705  /**
     706    If external plug-in JAR files should automatically be unloaded if the are modified.
     707    @since 2.4
     708  */
     709  static boolean autoUnloadPlugins()
     710  {
     711    return autoUnloadPlugins;
     712  }
     713 
     714 
     715  /**
    697716    Create a new <code>SessionControl</code> object. If BASE is not
    698717    running it will be started.
  • branches/webservices/src/core/net/sf/basedb/core/BioAssaySet.java

    r2998 r3653  
    313313    if (action == Transactional.Action.CREATE)
    314314    {
     315      checkAndCreateTables();
    315316      countSpotsAndReporters();
    316317    }
     
    11771178  }
    11781179 
     1180  private void checkAndCreateTables()
     1181  {
     1182    VirtualDb vdb = getVirtualDb();
     1183    vdb.createTables(VirtualTable.SPOT, VirtualTable.POSITION);
     1184    if (getDataCubeFilterNo() != 0)
     1185    {
     1186      vdb.createTables(VirtualTable.FILTER);
     1187    }
     1188  }
     1189 
    11791190  /**
    11801191    Called when a bioassayset is about to be deleted. Finds which data cubes, layers,
  • branches/webservices/src/core/net/sf/basedb/core/DataCube.java

    r3533 r3653  
    171171      getData().setBytes(addedBytes);
    172172      getData().setMaxRawMappingsForSpot(countSpotMappings());
     173      addedBytes = 0;
    173174    }
    174175    else if (action == Transactional.Action.UPDATE && addedBytes != 0)
     
    190191      query.setInteger("dataCube", getId());
    191192      query.executeUpdate();
     193      addedBytes = 0;
    192194    }
    193195  }
  • branches/webservices/src/core/net/sf/basedb/core/DbControl.java

    r3533 r3653  
    100100  /**
    101101    Lists items that are saved only if the parent item is also saved.
    102     @see #saveItemIf(BasicItem, BasicItem)
     102    @see #saveItemIf(BasicItem, BasicItem, boolean)
    103103  */
    104104  private Map<BasicItem, List<SaveIf>> saveIfQueue;
     
    356356          Map.Entry<BasicItem,Transactional.Action> entry = iterator.next();
    357357          BasicItem item = entry.getKey();
     358          Transactional.Action action = entry.getValue();
     359          if (afterCommitQueue.get(item) == action)
     360          {
     361            // Don't process the same item twice for the same action
     362            continue;
     363          }
    358364          BasicData data = item.getData();
    359           Transactional.Action action = entry.getValue();
    360365          boolean controlled = item instanceof Controlled;
    361366          boolean transactional = controlled && item instanceof Transactional;
     
    780785          item = c.newInstance(constructorParams);
    781786          itemCache.put(data, item);
     787          if (item instanceof Controlled)
     788          {
     789            commitQueue.put(item, Transactional.Action.UPDATE);
     790          }
    782791        }
    783792        catch (Exception ex)
     
    795804    item.initPermissions(0, 0);
    796805    item.checkPermission(Permission.READ);
    797     if (item instanceof Controlled)
    798     {
    799       commitQueue.put(item, Transactional.Action.UPDATE);
    800     }
    801806    return item;
    802807  }
     
    979984      }
    980985    }
     986  }
     987 
     988  /**
     989    Reload the item from the database. If the item isn't attached to this
     990    DbControl it is automatically reattaced first.
     991   
     992    @param item The item to reload
     993    @since 2.4
     994  */
     995  public void refreshItem(BasicItem item)
     996  {
     997    if (isClosed()) throw new ConnectionClosedException();
     998    sc.updateLastAccess();
     999    if (!isAttached(item)) reattachItem(item);
     1000    HibernateUtil.refresh(hSession, item.getData());
    9811001  }
    9821002 
  • branches/webservices/src/core/net/sf/basedb/core/Experiment.java

    r2694 r3653  
    237237    {
    238238      getData().setBytes(addedBytes);
     239      addedBytes = 0;
    239240    }
    240241    else if (action == Transactional.Action.UPDATE && addedBytes != 0)
     
    256257      query.setInteger("experiment", getId());
    257258      query.executeUpdate();
     259      addedBytes = 0;
    258260    }
    259261  }
  • branches/webservices/src/core/net/sf/basedb/core/ExtendedProperties.java

    r3581 r3653  
    2424package net.sf.basedb.core;
    2525
     26import net.sf.basedb.core.dbengine.DbEngine;
     27import net.sf.basedb.util.Values;
    2628import net.sf.basedb.util.XMLUtil;
    2729
     30import java.util.HashSet;
    2831import java.util.List;
    2932import java.util.ArrayList;
    3033import java.util.Map;
    3134import java.util.HashMap;
     35import java.util.Set;
     36import java.util.regex.PatternSyntaxException;
    3237import java.net.URL;
    3338
     
    194199    List<ExtendedProperty> properties = new ArrayList<ExtendedProperty>();
    195200    List<Element> children = (List<Element>)classElement.getChildren("property");
     201    DbEngine engine = HibernateUtil.getDbEngine();
     202    String className = classElement.getAttributeValue("name");
     203    Set<String> usedNames = new HashSet<String>();
    196204    for (Element property : children)
    197205    {
    198       String name = property.getAttributeValue("name");
    199       String title = property.getAttributeValue("title");
     206      String name = Values.getStringOrNull(property.getAttributeValue("name"));
     207      if (!ExtendedProperty.isValidName(name))
     208      {
     209        throw new InvalidDataException("Invalid property for class " +
     210          className + ": name=" + name);
     211      }
     212      if (usedNames.contains("name:" + name))
     213      {
     214        throw new InvalidDataException("Duplicate property for class " +
     215          className + ": name=" + name);
     216      }
     217      usedNames.add("name:" + name);
     218      String title = Values.getStringOrNull(property.getAttributeValue("title"));
    200219      if (title == null) title = name;
     220      String column = Values.getStringOrNull(property.getAttributeValue("column"));
     221      if (!engine.isValidColumnName(column))
     222      {
     223        throw new InvalidDataException("Invalid column for property " +
     224          className + "[" + name + "]: column=" + column);
     225      }
     226      if (usedNames.contains("column:" + column))
     227      {
     228        throw new InvalidDataException("Duplicate column for property " +
     229          className + "[" + name + "]: column=" + column);
     230      }
     231      usedNames.add("column:" + column);
     232      String description = Values.getStringOrNull(property.getAttributeValue("description"));
     233      int length = XMLUtil.getIntAttribute(property, "length", 255);
    201234      Type type = Type.fromValue(property.getAttributeValue("type"));
    202       String column = property.getAttributeValue("column");
    203       String description = property.getAttributeValue("description");
    204       int length = XMLUtil.getIntAttribute(property, "length", 255);
    205235      if (type == Type.STRING && length > 255) type = Type.TEXT;
    206236      boolean nullable = XMLUtil.getBooleanAttribute(property, "null", true);
     
    230260        for (Element link : links)
    231261        {
    232           String regexp = link.getAttributeValue("regexp");
    233           String url = link.getAttributeValue("url");
    234           epLinks.add(new ExtendedPropertyLinker(regexp, url));
     262          String regexp = Values.getStringOrNull(link.getAttributeValue("regexp"));
     263          String url = Values.getStringOrNull(link.getAttributeValue("url"));
     264          if (url == null)
     265          {
     266            throw new InvalidDataException("Missing url for property link " +
     267              className + "[" + name + "]: regexp=" + regexp);
     268          }
     269          try
     270          {
     271            epLinks.add(new ExtendedPropertyLinker(regexp, url));
     272          }
     273          catch (PatternSyntaxException ex)
     274          {
     275            throw new InvalidDataException("Invalid regexp for property link " +
     276              className + "[" + name + "]: regexp=" + regexp, ex);
     277          }
    235278        }
    236279      }
  • branches/webservices/src/core/net/sf/basedb/core/ExtendedProperty.java

    r3581 r3653  
    2626import java.text.NumberFormat;
    2727import java.util.List;
     28import java.util.regex.Pattern;
     29
    2830
    2931/**
     
    3739public class ExtendedProperty
    3840{
     41 
     42  /**
     43    A regexp checking for invalid characters.
     44  */
     45  private static final Pattern valid = Pattern.compile("[a-zA-Z_][a-zA-Z0-9_]*");
     46
     47  /**
     48    Check that the name only contains a-zA-Z0-9_ and starts with
     49    a letter or underscore.
     50    @since 2.4
     51  */
     52  public static boolean isValidName(String name)
     53  {
     54    return name == null ? false : valid.matcher(name).matches();
     55  }
     56 
    3957  private final String name;
    4058  private final Type type;
     
    196214    Numeric properties are parsed with the specified number format.
    197215    @param value The value to parse
    198     @param numberFormat The number format, or null to use Float.valueOf or Double.valueOf
     216    @param numberFormat The number format, or null to use Double.valueOf
    199217    @return An object
    200218    @throws InvalidDataException If the string cannot be converted to the correct type
     
    214232    parsed. Otherwise an exception is thrown.
    215233    @param value The value to parse
    216     @param numberFormat The number format, or null to use Float.valueOf or Double.valueOf
     234    @param numberFormat The number format, or null to use Double.valueOf
    217235    @param nullIfException TRUE to return null in case the string can't be parsed,
    218236      FALSE to throw an exception
  • branches/webservices/src/core/net/sf/basedb/core/Formula.java

    r3581 r3653  
    2424package net.sf.basedb.core;
    2525
     26import java.util.ArrayList;
    2627import java.util.Collections;
    2728import java.util.HashMap;
     
    166167  */
    167168  /**
    168     @see Type#validate(Formula)
     169    @see Formula.Type#validate(Formula)
    169170  */
    170171  @Override
     
    351352  public List<String> getFormulas()
    352353  {
    353     return Collections.unmodifiableList(getData().getFormulas());
     354    return Collections.unmodifiableList(new ArrayList<String>(getData().getFormulas()));
    354355  }
    355356 
     
    371372  /**
    372373    The average method used for the values of this formula. The average
    373     is only useful with a {@link Type#COLUMN_EXPRESSION}.
     374    is only useful with a {@link Formula.Type#COLUMN_EXPRESSION}.
    374375    @version 2.4
    375376  */
     
    378379    NONE(0, "None")
    379380    {
     381      @Override
    380382      public Expression getAverageExpression(Expression e)
    381383      {
     
    385387    GEOMETRIC_MEAN(1, "Geometric mean")
    386388    {
     389      @Override
    387390      public Expression getAverageExpression(Expression e)
    388391      {
     
    392395    ARITHMETIC_MEAN(2, "Arithmetic mean")
    393396    {
     397      @Override
    394398      public Expression getAverageExpression(Expression e)
    395399      {
     
    400404    MIN(3, "Min")
    401405    {
     406      @Override
    402407      public Expression getAverageExpression(Expression e)
    403408      {
     
    408413    MAX(4, "Max")
    409414    {
     415      @Override
    410416      public Expression getAverageExpression(Expression e)
    411417      {
  • branches/webservices/src/core/net/sf/basedb/core/HibernateUtil.java

    r3533 r3653  
    138138
    139139  /**
    140     Initialise this class. This is done at startup time by the
    141     {@link Application#start()} method. Initialising means that we
     140    First step of initialising this class. This is done at startup time by the
     141    {@link Application#start()} method. In this step we load configuration
     142    settings from the 'base.config' and 'hibernate.cfg.xml' files and
     143    create the Dialect and DbEngine objects.
     144   
     145    Initialising means that we
    142146    load the configuration from the properties and the xml file,
    143147    read all mapping files, generate additional mappings for the
     
    145149    used by {@link Query} implementation.
    146150  */
    147   static synchronized void init()
     151  static synchronized void init1()
    148152    throws BaseException
    149153  {
     
    155159      cfg = new Configuration();
    156160      setConfigurationProperties(cfg);
     161      dialect = Dialect.getDialect(cfg.getProperties());
     162      dbEngine = EngineFactory.createEngine(dialect);
     163    }
     164    catch (HibernateException ex)
     165    {
     166      throw new BaseException(ex);
     167    }
     168  }
     169
     170  /**
     171    Second step of initialising this class. This is done at startup time by the
     172    {@link Application#start()} method. In this step we read all mapping files,
     173    generate additional mappings for the {@link ExtendableData} items and raw data,
     174    and generate filters  used by {@link Query} implementation.
     175  */
     176  static synchronized void init2()
     177    throws BaseException
     178  {
     179    // Return if we have already been initialised
     180    if (isInitialised) return;
     181 
     182    try
     183    {
    157184      addStaticMappings(cfg);
    158185      addExtendedPropertiesMappings(cfg);
     
    161188      cfg.configure();
    162189      sf = cfg.buildSessionFactory();
    163       dialect = Dialect.getDialect(cfg.getProperties());
    164       dbEngine = EngineFactory.createEngine(dialect);
    165190    }
    166191    catch (HibernateException ex)
     
    170195    isInitialised = true;
    171196  }
    172 
     197 
    173198  /**
    174199    Unload all settings.
     
    10881113
    10891114  /**
     1115    Reload the data from the database for a given entity.
     1116    @param session The Hibernate session which is connected to the
     1117      database
     1118    @param data The entity to reload
     1119    @since 2.4
     1120  */
     1121  static void refresh(Session session, BasicData data)
     1122  {
     1123    assert session != null : "session == null";
     1124    try
     1125    {
     1126      session.refresh(data);
     1127    }
     1128    catch(HibernateException ex)
     1129    {
     1130      throw new BaseException(ex);
     1131    }   
     1132  }
     1133 
     1134  /**
    10901135    Checks if an item with the specified ID exists in the database.
    10911136    @param session The Hibernate session which is connected to the
     
    13301375    assert session != null : "session == null";
    13311376    assert sql != null : "sql == null";
     1377    sql = sql.replace('[', getDialect().openQuote()).replace(']', getDialect().closeQuote());
    13321378    try
    13331379    {
     
    13481394    assert session != null : "session == null";
    13491395    assert sql != null : "sql == null";
     1396    sql = sql.replace('[', getDialect().openQuote()).replace(']', getDialect().closeQuote());
    13501397    try
    13511398    {
  • branches/webservices/src/core/net/sf/basedb/core/Install.java

    r3581 r3653  
    3131import net.sf.basedb.core.data.HardwareTypeData;
    3232import net.sf.basedb.core.data.MimeTypeData;
     33import net.sf.basedb.core.data.PluginConfigurationData;
    3334import net.sf.basedb.core.data.ProtocolTypeData;
    3435import net.sf.basedb.core.data.QuotaData;
     
    101102    method.
    102103  */
    103   public static final int NEW_SCHEMA_VERSION = Integer.valueOf(37).intValue();
     104  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(40).intValue();
    104105 
    105106  public static synchronized void createTables(boolean update, final ProgressReporter progress)
     
    151152    required for BASE to work properly. Items that already exists
    152153    will not be modified.
    153 
     154 
    154155    @param progress An object implementing the {@link ProgressReporter}
    155156      interface
     
    166167      Application.start(false, false, false);
    167168      session = HibernateUtil.newSession();
    168 
     169 
    169170      // SchemaVersion
    170171      schemaVersion = createSchemaVersion(update ? 1 : NEW_SCHEMA_VERSION);
    171 
     172 
    172173      // QuotaTypes
    173174      if (progress != null) progress.display((int)(1*progress_factor), "--Creating quota types...");
     
    176177      createQuotaType(QuotaType.RAW_DATA, "Raw data", "Quota for raw data", false);
    177178      createQuotaType(QuotaType.EXPERIMENT, "Experiment", "Quota for experiment", false);
    178 
     179 
    179180      // Quota
    180181      if (progress != null) progress.display((int)(2*progress_factor), "--Creating quota...");
     
    186187      QuotaData quota1000 = createQuota(null, "1 GB total", "1 GB total quota.", 1024*1024*1024);
    187188      QuotaData quota0 = createQuota(null, "No quota", "May not consume any disk space at all", 0);
    188 
     189 
    189190      // Roles
    190191      if (progress != null) progress.display((int)(3*progress_factor), "--Creating roles...");
     
    195196      RoleData roleGuest = createRole(Role.GUEST, "Guest", false, "For users wanting to have a peek at BASE. Has very limited access to create new things.");
    196197      RoleData roleJobAgent = createRole(Role.JOBAGENT, "Job agent", false, "This role is given to job agents and allows them to read and execute jobs.");
    197 
     198 
    198199      // Users
    199200      if (progress != null) progress.display((int)(4*progress_factor), "--Creating users...");
     
    207208      // createUser(0, "demo", "demo", "Demo", "This account can be used for demonstration purposes.", Role.GUEST);
    208209      // createUser(0, "power", "power", "Power user", "This account has power user privileges.", Role.POWER_USER);
    209 
     210 
    210211      // Now that we have a root user let's create a session
    211212      sessionControl = Application.newSessionControl( null, null, null );
    212213      sessionControl.login(rootLogin, rootPassword, "InitDBSessionId", false);
    213 
     214 
    214215      if (progress != null) progress.display((int)(5*progress_factor), "--Creating groups...");
    215216      GroupData groupEveryone = createGroup(Group.EVERYONE, "Everyone", false, "Everyone are members of this group.");
    216 
     217 
    217218      if (progress != null) progress.display((int)(6*progress_factor), "--Creating keys...");
    218219      int PERMISSION_ALL = Permission.grant(Permission.READ, Permission.USE, Permission.WRITE,
     
    228229      administrators_all.put(roleAdmin, PERMISSION_ALL);
    229230      administrators_all.put(roleSuper, PERMISSION_READ);
    230 
     231 
    231232      // Administrators -> WRITE
    232233      HashMap<RoleData, Integer> administrators_write = new HashMap<RoleData, Integer>();
    233234      administrators_write.put(roleAdmin, PERMISSION_WRITE);
    234235      administrators_write.put(roleSuper, PERMISSION_READ);
    235 
     236 
    236237      // Administrators -> READ
    237238      HashMap<RoleData, Integer> administrators_read = new HashMap<RoleData, Integer>();
    238239      administrators_read.put(roleAdmin, PERMISSION_READ);
    239240      administrators_read.put(roleSuper, PERMISSION_READ);
    240 
     241 
    241242      // Power users -> CREATE; Administrators -> ALL
    242243      HashMap<RoleData, Integer> power_users_create = new HashMap<RoleData, Integer>();
     
    244245      power_users_create.put(rolePower, PERMISSION_CREATE);
    245246      power_users_create.put(roleSuper, PERMISSION_READ);
    246 
     247 
    247248      // Power users & Users -> CREATE; Administrators -> ALL
    248249      HashMap<RoleData, Integer> users_create = new HashMap<RoleData, Integer>();
     
    251252      users_create.put(roleUser, PERMISSION_CREATE);
    252253      users_create.put(roleSuper, PERMISSION_READ);
    253 
     254 
    254255      // Power users & Users & Guests -> CREATE; Administrators -> ALL
    255256      HashMap<RoleData, Integer> guests_create = new HashMap<RoleData, Integer>();
     
    259260      guests_create.put(roleGuest, PERMISSION_CREATE);
    260261      guests_create.put(roleSuper, PERMISSION_READ);
    261 
     262 
    262263      // All -> CREATE; Administrators -> ALL
    263264      HashMap<RoleData, Integer> all_create = new HashMap<RoleData, Integer>();
     
    275276      all_use_administrators_write.put(roleGuest, PERMISSION_USE);
    276277      all_use_administrators_write.put(roleSuper, PERMISSION_USE);
    277 
     278 
    278279      // Users & Guests & Powers users -> USE; Administrators -> ALL
    279280      HashMap<RoleData, Integer> guests_use_administrators_all = new HashMap<RoleData, Integer>();
     
    283284      guests_use_administrators_all.put(roleGuest, PERMISSION_USE);
    284285      guests_use_administrators_all.put(roleSuper, PERMISSION_READ);
    285 
     286 
    286287      // Users & Guests -> USE; Powers users & Administrators -> ALL
    287288      HashMap<RoleData, Integer> guests_use_power_users_all = new HashMap<RoleData, Integer>();
     
    304305      createRoleKey(Item.USER, "Users", "Gives access to users.", administrators_all);
    305306      createRoleKey(Item.PROJECT, "Projects", "Gives access to projects.", users_create);
    306 
     307 
    307308      // Files, directories and quota
    308309      createRoleKey(Item.DIRECTORY, "Directories", "Gives access to directories", guests_create);
     
    312313      createRoleKey(Item.QUOTA, "Quota", "Gives access to quota", administrators_all);
    313314      createRoleKey(Item.DISKUSAGE, "Disc usage", "Gives access disc usage", administrators_read);
    314 
     315 
    315316      // Protocols, hardware, software
    316317      createRoleKey(Item.PROTOCOLTYPE, "Protocol types", "Gives access to protocol types", guests_use_power_users_all);
     
    320321      createRoleKey(Item.SOFTWARETYPE, "Software types", "Gives access to software types", all_use_administrators_write);
    321322      createRoleKey(Item.SOFTWARE, "Software", "Gives access to software", power_users_create);
    322 
     323 
    323324      // Annotations
    324325      createRoleKey(Item.ANNOTATIONTYPE, "Annotation types", "Gives access to annotation types", power_users_create);
     
    331332      createRoleKey(Item.EXTRACT, "Extracts", "Gives access to extracts", users_create);
    332333      createRoleKey(Item.LABELEDEXTRACT, "Labeled extracts", "Gives access to labeled extracts", users_create);
    333 
     334 
    334335      // Reporters
    335336      createRoleKey(Item.REPORTERTYPE, "Reporter types", "Gives access to reporter types", guests_use_power_users_all);
    336337      createRoleKey(Item.REPORTER, "Reporters", "Gives access to reporter", guests_use_power_users_all);
    337338      createRoleKey(Item.REPORTERLIST, "Reporter lists", "Gives access to reporter lists", users_create);
    338 
     339 
    339340      // Array LIMS - plates
    340341      createRoleKey(Item.PLATEGEOMETRY, "Plate geometries", "Gives access to plate geometries", guests_use_administrators_all);
     
    342343      createRoleKey(Item.PLATE, "Plates", "Gives access to plates", power_users_create);
    343344      createRoleKey(Item.PLATEMAPPING, "Plate mappings", "Gives access to plate mappings", power_users_create);
    344 
     345 
    345346      // Array LIMS - arrays
    346347      createRoleKey(Item.ARRAYDESIGN, "Array design", "Gives access to array designs", power_users_create);
    347348      createRoleKey(Item.ARRAYBATCH, "Array batches", "Gives access to array batches", power_users_create);
    348349      createRoleKey(Item.ARRAYSLIDE, "Array slides", "Gives access to array slides", power_users_create);
    349 
     350 
    350351      // Hybridization, raw data and experiments
    351352      createRoleKey(Item.HYBRIDIZATION, "Hybridizations", "Gives access to hybridizations", users_create);
     
    355356      createRoleKey(Item.FORMULA, "Formulas", "Gives access to formulas", users_create);
    356357      createRoleKey(Item.EXTRAVALUETYPE, "Extra value types", "Gives access to extra value types", guests_use_power_users_all);
    357 
     358 
    358359      // Plugins, jobs
    359360      createRoleKey(Item.PLUGINTYPE, "Plugin types", "Gives access to plugin types", administrators_all);
     
    362363      createRoleKey(Item.JOB, "Jobs", "Gives access to jobs", guests_create);
    363364      createRoleKey(Item.JOBAGENT, "Job agents", "Gives access to job agents", administrators_all);
    364 
     365 
    365366      // Misc.
    366367      createRoleKey(Item.CLIENT, "Client applications", "Gives access to client applications", administrators_all);
     
    370371      createRoleKey(Item.SETTING, "Settings", "Gives access to settings", administrators_all);
    371372      createRoleKey(Item.MESSAGE, "Messages", "Gives access to messages", users_create);
    372 
     373 
    373374      // Permissions for job agents are only added for new installations and
    374375      // updates below schema version 13
     
    395396      ItemKeyData keyEveryoneUse = createItemKey("EVERYONE=USE", null, everyoneUse);
    396397      ItemKeyData keyJobAgentUse = createItemKey("JOBAGENT=USE", jobAgentUse, null);
    397 
     398 
    398399      // ProtocolTypes
    399400      if (progress != null) progress.display((int)(7*progress_factor), "--Creating protocol types...");
     
    406407      createProtocolType(ProtocolType.SCANNING, "Scanning", "Protocols used for scanning microarray images.");
    407408      createProtocolType(ProtocolType.FEATURE_EXTRACTION, "Feature extraction", "Protocols used for extracting features from microarray images.");
    408 
     409 
    409410      // HardwareTypes
    410411      if (progress != null) progress.display((int)(8*progress_factor), "--Creating hardware types...");
     
    412413      HardwareTypeData robot = createHardwareType(HardwareType.PRINT_ROBOT, "Print robot", "Spot the probe on the array.");
    413414      HardwareTypeData hybStation = createHardwareType(HardwareType.HYBRIDIZATION_STATION, "Hybridization station", "Automate the hybridization of microarrays on slides.");
    414 
     415 
    415416      // Hardware
    416417      if (progress != null) progress.display((int)(9*progress_factor), "--Creating hardware...");
     
    425426      createHardware("OmniGrid", "100", "", robot, rootUser, keyEveryoneUse);
    426427      createHardware("Qarray", "Max", "", robot, rootUser, keyEveryoneUse);
    427 
     428 
    428429      // SoftwareTypes
    429430      if (progress != null) progress.display((int)(10*progress_factor), "--Creating software types...");
    430431      SoftwareTypeData feature = createSoftwareType(SoftwareType.FEATURE_EXTRACTION, "Feature extraction", "Extracts features from microarray images.");
    431 
     432 
    432433      // Software
    433434      if (progress != null) progress.display((int)(11*progress_factor), "--Creating software...");
     
    442443      createSoftware("ScanArray", null, null, feature, rootUser, keyEveryoneUse);
    443444      createSoftware("Affymetrix GeneChip Software", "1.2", null, feature, rootUser, keyEveryoneUse);
    444 
     445      createSoftware("Illumina BeadStudio", null, null, feature, rootUser, keyEveryoneUse);
     446 
    445447      // Directory
    446448      if (progress != null) progress.display((int)(12*progress_factor), "--Creating directories...");
     
    451453      createDirectory(rootUser, templateDirectory, null, "raw data", "Place your raw data files here", null);
    452454      createDirectory(rootUser, templateDirectory, null, "projects", "Create a subdirectory for project-related files in this directory.", null);
    453 
     455 
    454456      // FileTypes
    455457      if (progress != null) progress.display((int)(13*progress_factor), "--Creating file types...");
     
    463465      FileTypeData imageType = createFileType(FileType.IMAGE, "Image", "Image files");
    464466      createFileType(FileType.SPOT_IMAGES, "Spot images", "A zip file containing generated spot images in png format.");
    465 
     467 
    466468      // MimeTypes
    467469      if (progress != null) progress.display((int)(14*progress_factor), "--Creating MIME types...");
     
    505507      createMimeType("application/x-gtar", "Gzipped archive", "gtar", null);
    506508      createMimeType("application/x-gzip", "Gzip compressed file", "gz", null);
    507 
     509 
    508510      // Microarray/BASE-specific mime types
    509511      createMimeType("text/plain", "GenePix Results file", "gpr", rawDataType);
     
    517519      createMimeType("text/plain", "Biorobotics TAM format", "tam", printMapType);
    518520      createMimeType("text/plain", "Molecularware MWBR format", "mvbr", printMapType);
    519 
     521 
    520522      // Plate geometries
    521523      if (progress != null) progress.display((int)(15*progress_factor), "--Creating plate geometries...");
     
    523525      PlateGeometryData plate384 = createPlateGeometry("384-well (16 x 24)", "384-wells, 16 rows, 24 columns", 16, 24);
    524526      PlateGeometryData plate1536 = createPlateGeometry("1536-well (32 x 48)", "1536-wells, 32 rows, 48 columns", 32, 48);
    525 
     527 
    526528      // Plate mappings
    527529      if (progress != null) progress.display((int)(16*progress_factor), "--Creating plate mappings...");
     
    536538      createPlateMapping("1536 --> 1536", "Maps 1:1 between 1536-well (16 x 24) plates",
    537539        plate1536, 1, plate1536, 1, null, rootUser, keyEveryoneUse);
    538 
    539 
     540 
     541 
    540542      // Labels
    541543      if (progress != null) progress.display((int)(17*progress_factor), "--Creating labels...");
     
    556558      createAnnotationType("Comment", "", Type.STRING, 1, null,
    557559        wells, null, false, false, rootUser, keyEveryoneUse );
    558 
     560 
    559561      // Clients
    560562      if (progress != null) progress.display((int)(19*progress_factor), "--Creating clients...");
     
    562564      createClient(rootUser, "net.sf.basedb.clients.migration", "Migration tool", "This client is used to migrate BASE 1.2.x data to BASE 2", null);
    563565      createClient(rootUser, "net.sf.basedb.clients.jobagent", "Job agent client", "This client is used by all job agents", keyJobAgentUse);
    564 
     566 
    565567      // News
    566568      if (progress != null) progress.display((int)(20*progress_factor), "--Creating news...");
    567569      createNews("BASE 2 Server installed", "Welcome to your new BASE 2 server.");
    568 
     570 
    569571      // Plugins
    570572      if (progress != null) progress.display((int)(21*progress_factor), "--Creating plugin definitions...");
     
    581583        "file system  first. For this to work the plugin must also be given 'immediate exection' rights",
    582584        "net.sf.basedb.core.plugin.ImmediateDownloadExporter", null);
    583 
     585      createPluginType("Analysis filter plug-in", "Analysis plug-ins that are pure filter plug-ins should " +
     586          "implement this interface. If they do they are linked with the 'Filter bioassayset' button and" +
     587          "not just the 'Run analysis plug-in' button.",
     588          "net.sf.basedb.core.plugin.AnalysisFilterPlugin", null);
     589     
    584590      createPluginDefinition("net.sf.basedb.plugins.Base1PluginExecuter", null, null, true, null, false);
    585591      createPluginDefinition("net.sf.basedb.plugins.BioAssaySetExporter", null, keyEveryoneUse, true, null, true);
     
    606612      createPluginDefinition("net.sf.basedb.plugins.CdfFileReporterImporter", null, null, true, null, false);
    607613      createPluginDefinition("net.sf.basedb.plugins.PackedFileExporter", null, keyEveryoneUse, true, null, true);
     614      createPluginDefinition("net.sf.basedb.plugins.AnnotationFlatFileImporter", null, keyEveryoneUse, true, null, false);
     615      createPluginDefinition("net.sf.basedb.plugins.IlluminaRawDataImporter", null, keyEveryoneUse, true, null, false);
    608616     
    609617      // Plugin configurations
    610       if (!update)
    611       {
    612         if (progress != null) progress.display((int)(22*progress_factor), "--Creating example plugin configurations...");
    613         createPluginConfigurations("/plugin_configfile.xml", update);
    614       }
    615 
     618      if (progress != null) progress.display((int)(22*progress_factor), "--Creating example plugin configurations...");
     619      createPluginConfigurations("/plugin_configfile.xml", update);
     620      createPluginConfigurations("/illumina.configurations.xml", update);
     621     
     622 
    616623      // Formulas
    617624      ColoringData NO_COLORING = new ColoringData(false, false, null, null, null);
     
    630637        "Swap channel 1 and 2", "Swaps the intensities in channel 1 and 2", null, 2,
    631638        new String[] { "ch(2)", "ch(1)" }, NO_COLORING, rootUser, keyEveryoneUse);
    632 
     639 
    633640      // Intensity expression formulas defined by raw data types
    634641      int maxChannels = 0;
     
    655662          null, channel, new String[] { expression }, NO_COLORING, rootUser, keyEveryoneUse);
    656663      }
    657 
     664 
    658665      if (progress != null) progress.display((int)(24*progress_factor), "--Creating job agents...");
    659666      // TODO
     
    19181925      {
    19191926        int version = schemaVersion.getSchemaVersion();
    1920         pd.loadPluginInformation(jarPath, className, version < 20);
     1927        pd.loadPluginInformation(jarPath, className, true);
    19211928        if (version < 21) pd.setAllowImmediateExecution(allowImmediateExecution);
    19221929        dc.commit();
     
    19551962    DbControl dc = null;
    19561963   
    1957     // Only get configurations from file if it's an installation of BASE2 and never if it's an update.
    1958     if (!update)
    1959     {
    1960       try
    1961       {
    1962         dc = sessionControl.newDbControl();
    1963         URL dtdURL = Install.class.getResource("/net/sf/basedb/core/dtd/plugin-configuration-file.dtd");
     1964    try
     1965    {
     1966      dc = sessionControl.newDbControl();
     1967     
     1968      org.hibernate.Query query = null;
     1969      if (update)
     1970      {
     1971        // If we are updating, we must check if a configuration with a
     1972        // given name already exists
     1973        query = HibernateUtil.getPredefinedQuery(dc.getHibernateSession(),
     1974          "GET_PLUGINCONFIGURATION_FOR_PLUGIN_WITH_NAME");
     1975        /*
     1976          SELECT pc
     1977          FROM PluginConfigurationData pc
     1978          WHERE pc.pluginDefinition.className = :className
     1979          AND pc.name = :name
     1980        */
     1981      }
     1982     
     1983      URL dtdURL = Install.class.getResource("/net/sf/basedb/core/dtd/plugin-configuration-file.dtd");
     1984      URL fileURL = Install.class.getResource(filePath);
     1985      Document doc = XMLUtil.getValidatedXml(fileURL, dtdURL);
     1986      Element rootElement = doc.getRootElement();   
     1987     
     1988      List configurations = rootElement.getChildren();
     1989     
     1990      for (Object obj : configurations)
     1991      {
     1992        Element configuration = (Element)obj;
     1993        String name = configuration.getChildText("configname");
     1994        String description = configuration.getChildText("description");
     1995        String pluginClassName = configuration.getAttributeValue("pluginClassName");
    19641996       
    1965         Document doc = XMLUtil.getValidatedXML(Install.class.getResourceAsStream(filePath), dtdURL);     
    1966         Element rootElement = doc.getRootElement();   
     1997        if (update)
     1998        {
     1999          // Check if it already exists
     2000          query.setString("className", pluginClassName);
     2001          query.setString("name", name);
     2002          PluginConfigurationData config = HibernateUtil.loadData(PluginConfigurationData.class, query);
     2003         
     2004          if (config != null)
     2005          {
     2006            log.info("createPluginConfigurations: EXISTS [plugin="+pluginClassName+
     2007                "; name=" + name + "]");
     2008            continue;
     2009            // Continue with next configuration
     2010          }
     2011        }
    19672012       
    1968         List configurations = rootElement.getChildren();
    1969        
    1970         for (Object obj : configurations)
     2013        try
    19712014        {
    1972           Element configuration = (Element)obj;
    1973           String name = configuration.getChildText("configname");
    1974           String description = configuration.getChildText("description");
    1975           String pluginClassName = configuration.getAttributeValue("pluginClassName");
     2015          PluginDefinition pluginDefinition = PluginDefinition.getByClassName(dc, pluginClassName);
     2016                             
     2017          // Create a new plugin configurationj
     2018          PluginConfiguration pluginConfig = PluginConfiguration.getNew(dc, pluginDefinition); 
     2019          pluginConfig.setItemKey(pluginDefinition.getItemKey());
     2020          pluginConfig.setProjectKey(pluginDefinition.getProjectKey());
     2021          dc.saveItem(pluginConfig);
     2022          pluginConfig.setName(name);
     2023          pluginConfig.setDescription(description);
    19762024         
    1977           try
    1978           {
    1979             PluginDefinition pluginDefinition = PluginDefinition.getByClassName(dc, pluginClassName);
    1980                                
    1981             // Create a new plugin configurationj
    1982             PluginConfiguration pluginConfig = PluginConfiguration.getNew(dc, pluginDefinition);           
    1983             dc.saveItem(pluginConfig);
    1984             pluginConfig.setName(name);
    1985             pluginConfig.setDescription(description);
     2025          // Get the confiuration parameters from file
     2026          List parameters = configuration.getChildren("parameter");
     2027          for (Object elementObj : parameters)
     2028          {
     2029            Element parameter = (Element)elementObj;
     2030            String parametername = parameter.getChildText("name");               
     2031            String cl = parameter.getChildText("class");
     2032            String label = parameter.getChildText("label").length() > 0 ? parameter.getChildText("label") : name;         
     2033            Class clazz = null;
     2034            List<Object> values = new ArrayList<Object>() ;
    19862035           
    1987             // Get the confiuration parameters from file
    1988             List parameters = configuration.getChildren("parameter");
    1989             for (Object elementObj : parameters)
     2036            if (cl.length() > 0)
    19902037            {
    1991               Element parameter = (Element)elementObj;
    1992               String parametername = parameter.getChildText("name");               
    1993               String cl = parameter.getChildText("class");
    1994               String label = parameter.getChildText("label").length() > 0 ? parameter.getChildText("label") : name;         
    1995               Class clazz = null;
    1996               List<Object> values = new ArrayList<Object>() ;
    1997              
    1998               if (cl.length() > 0)
    1999               {
    2000                 clazz = Class.forName(cl);
    2001                 List children = parameter.getChildren("value");
    2002                 // Get the parameter values
    2003                 for (Object ch : children)
    2004                 {
    2005                   String text = ((Element)ch).getText();
    2006                   if (clazz.equals(Boolean.class)) values.add(new Boolean(text));
    2007                   else if (clazz.equals(Date.class)) values.add(DateUtil.parseString(text));
    2008                   else if (clazz.equals(Double.class)) values.add(new Double(text));
    2009                   else if (clazz.equals(Float.class)) values.add(new Float(text));
    2010                   else if (clazz.equals(Long.class)) values.add(new Long(text));
    2011                   else if (clazz.equals(String.class)) values.add(text);
    2012                 }   
    2013                 // Get the parametertype
    2014                 ParameterType pType;
    2015                 if (clazz.equals(Boolean.class)) pType = new BooleanParameterType();
    2016                 else if (clazz.equals(Date.class)) pType =  new DateParameterType();
    2017                 else if (clazz.equals(Double.class)) pType =  new DoubleParameterType();   
    2018                 else if (clazz.equals(Float.class)) pType =  new FloatParameterType();
    2019                 else if (clazz.equals(Integer.class)) pType =  new IntegerParameterType();   
    2020                 else if (clazz.equals(Long.class)) pType =  new LongParameterType();
    2021                 else if (clazz.equals(String.class)) pType =  new StringParameterType();
    2022                 else pType = null;
    2023                 pluginConfig.setParameterValues(parametername,label, "", pType, values);
    2024               }
    2025             }         
    2026           }       
    2027           catch(Throwable ex)
    2028           {
    2029             log.error("createPluginConfiguration: FAILED[Configuration: " + name, ex);         
    2030           }
     2038              clazz = Class.forName(cl);
     2039              List children = parameter.getChildren("value");
     2040              // Get the parameter values
     2041              for (Object ch : children)
     2042              {
     2043                String text = ((Element)ch).getText();
     2044                if (clazz.equals(Boolean.class)) values.add(new Boolean(text));
     2045                else if (clazz.equals(Date.class)) values.add(DateUtil.parseString(text));
     2046                else if (clazz.equals(Double.class)) values.add(new Double(text));
     2047                else if (clazz.equals(Float.class)) values.add(new Float(text));
     2048                else if (clazz.equals(Long.class)) values.add(new Long(text));
     2049                else if (clazz.equals(String.class)) values.add(text);
     2050              }   
     2051              // Get the parametertype
     2052              ParameterType pType;
     2053              if (clazz.equals(Boolean.class)) pType = new BooleanParameterType();
     2054              else if (clazz.equals(Date.class)) pType =  new DateParameterType();
     2055              else if (clazz.equals(Double.class)) pType =  new DoubleParameterType();   
     2056              else if (clazz.equals(Float.class)) pType =  new FloatParameterType();
     2057              else if (clazz.equals(Integer.class)) pType =  new IntegerParameterType();   
     2058              else if (clazz.equals(Long.class)) pType =  new LongParameterType();
     2059              else if (clazz.equals(String.class)) pType =  new StringParameterType();
     2060              else pType = null;
     2061              pluginConfig.setParameterValues(parametername,label, "", pType, values);
     2062            }
     2063          }         
    20312064        }       
    2032         dc.commit();
    2033       }
    2034       catch(Throwable ex)
    2035       {
    2036         throw new BaseException(ex);
    2037       }
    2038       finally
    2039       {
    2040         if (dc != null) dc.close();
    2041       }
     2065        catch(Throwable ex)
     2066        {
     2067          log.error("createPluginConfiguration: FAILED[Configuration: " + name, ex);         
     2068        }
     2069      }       
     2070      dc.commit();
     2071    }
     2072    catch(Throwable ex)
     2073    {
     2074      throw new BaseException(ex);
     2075    }
     2076    finally
     2077    {
     2078      if (dc != null) dc.close();
    20422079    }
    20432080  }
  • branches/webservices/src/core/net/sf/basedb/core/Item.java

    r3533 r3653  
    623623    Get a value indicating the deletion order. Items with a low value
    624624    should be deleted before items with a high value, to minimize the risk
    625     that the {@lin BasicItem#isUsed()} method returns true.
     625    that the {@link BasicItem#isUsed()} method returns true.
    626626    @return The deletion order value
    627627    @since 2.4
  • branches/webservices/src/core/net/sf/basedb/core/ItemContext.java

    r3533 r3653  
    165165  private final Item itemType;
    166166  private final String subContext;
     167  private int contextId;
    167168  private int itemId;
    168169  private Set<Integer> selected;
     
    218219    this.subContext = context.getSubContext();
    219220    this.name = context.getName();
     221    this.contextId = context.getId();
    220222    this.itemId = context.getItemId();
    221223    this.rowsPerPage = context.getRowsPerPage();
     
    295297  }
    296298
     299  /**
     300    Get the database ID of this context. Can be used to load contexts
     301    @return The database ID of the context, or 0 if it hasn't been saved to
     302      the database
     303    @since 2.4
     304  */
     305  public int getContextId()
     306  {
     307    return contextId;
     308  }
     309 
    297310  /**
    298311    Get the ID of the current item in this context.
  • branches/webservices/src/core/net/sf/basedb/core/ItemInUseException.java

    r2304 r3653  
    4848    super("The item "+what+" is used by another item.");
    4949  }
     50 
     51  /**
     52    Creates a new <code>ItemInUseException</code> with a cause. The error
     53    message produced will look like:
     54    <code>Permission denied. The item User[ID=325] is used by another item.</code>
     55 
     56    @param what A description of what already exists, for
     57      example User[Id=325]
     58    @param cause The cause of the error
     59    @since 2.4
     60  */
     61  public ItemInUseException(String what, Throwable cause)
     62  {
     63    super("The item "+what+" is used by another item.", cause);
     64  }
     65 
    5066}
  • branches/webservices/src/core/net/sf/basedb/core/Job.java

    r3533 r3653  
    2525
    2626import net.sf.basedb.core.Transactional.Action;
     27import net.sf.basedb.core.data.ExperimentData;
    2728import net.sf.basedb.core.data.JobData;
    2829import net.sf.basedb.core.data.MessageData;
     
    283284    }
    284285  }
     286  /**
     287    Grant read permission if the logged in user has read permission to the
     288    experiment the job belongs to.
     289  */
     290  @Override
     291  void initPermissions(int granted, int denied)
     292  {
     293    ExperimentData parent = getData().getExperiment();
     294    if (parent != null)
     295    {
     296      int parentPermission = 0;
     297      if (parent.getId() != 0)
     298      {
     299        parentPermission = getSessionControl().getAllPermissions(parent);
     300      }
     301      else
     302      {
     303        BasicItem<?> basicParent = getDbControl().getItem(BasicItem.class, parent);
     304        parentPermission = Permission.grant(basicParent.getPermissions());
     305      }
     306      if (Permission.hasPermission(parentPermission, Permission.READ))
     307      {
     308        granted |= Permission.grant(Permission.READ);
     309      }
     310    }
     311    super.initPermissions(granted, denied);
     312  }
    285313  // -------------------------------------------
    286314
     
    351379      getData().setPluginConfiguration(pluginConfiguration.getData());
    352380      getData().setParameterVersion(pluginConfiguration.getParameterVersion());
     381    }
     382  }
     383 
     384  /**
     385    Get the experiment this job is a part of.
     386    @return The <code>Experiment</code> item, or null if this job
     387      isn't part of an experiment
     388    @since 2.4
     389  */
     390  public Experiment getExperiment()
     391  {
     392    return getDbControl().getItem(Experiment.class, getData().getExperiment());     
     393  }
     394  /**
     395    Set the experiment this job is part of. Once an experiment has been set, it
     396    can't be changed.
     397    @since 2.4
     398  */
     399  void setExperiment(Experiment experiment)
     400  {
     401    ExperimentData current = getData().getExperiment();
     402    ExperimentData next = experiment == null ? null : experiment.getData();
     403    if (current == null)
     404    {
     405      getData().setExperiment(next);
     406    }
     407    else if (!current.equals(next))
     408    {
     409      throw new PermissionDeniedException("A job can only be part of one experiment: " + this);
    353410    }
    354411  }
  • branches/webservices/src/core/net/sf/basedb/core/PluginDefinition.java

    r3533 r3653  
    973973      {
    974974        if (unloadBefore) JarClassLoader.unload(jarPath);
    975         ClassLoader cl = JarClassLoader.getInstance(jarPath);
     975        ClassLoader cl = JarClassLoader.getInstance(jarPath, Application.autoUnloadPlugins());
    976976        c = cl.loadClass(className);
    977977      }
  • branches/webservices/src/core/net/sf/basedb/core/PluginRequest.java

    r2981 r3653  
    146146  }
    147147 
     148  /**
     149    Get the values that are currently stored in the job or plugin configuration
     150    related to this request. This method will first check the job and then the
     151    plugin configuration.
     152    @param name The name of the parameter
     153    @return The parameter values, or null if no parameter with the given name
     154      exists
     155  */
    148156  public List<?> getCurrentParameterValues(String name)
    149157  {
     
    153161      values = jobParameters.getValues(name);
    154162    }
    155     else if (configurationParameters != null)
     163    if (values == null && configurationParameters != null)
    156164    {
    157165      values = configurationParameters.getValues(name);
     
    161169 
    162170 
     171  /**
     172    Get the values that are currently stored in the plugin configuration
     173    related to this request.
     174    @param name The name of the parameter
     175    @return The parameter values, or null if no parameter with the given name
     176      exists or if this request isn't associated with a plugin configuration
     177  */
    163178  public List<?> getCurrentConfigurationParameterValues(String name)
    164179  {
     
    171186  }
    172187 
     188  /**
     189    Get the values that are currently stored in the job related to this
     190    request.
     191    @param name The name of the parameter
     192    @return The parameter values, or null if no parameter with the given name
     193      exists or if this request isn't associated with a job
     194  */
    173195  public List<?> getCurrentJobParameterValues(String name)
    174196  {
  • branches/webservices/src/core/net/sf/basedb/core/PluginType.java

    r3533 r3653  
    269269      {
    270270        JarClassLoader.unload(jarPath);
    271         ClassLoader cl = JarClassLoader.getInstance(jarPath);
     271        ClassLoader cl = JarClassLoader.getInstance(jarPath, Application.autoUnloadPlugins());
    272272        c = cl.loadClass(interfaceName);
    273273      }
  • branches/webservices/src/core/net/sf/basedb/core/Project.java

    r3533 r3653  
    363363    @param firstItem The index of the first item to return (0-based)
    364364    @param maxItems The maximum number of items to return, or 0 to return all items
    365     @param permissions The permission the logged in user must have on the item
     365    @param permission The permission the logged in user must have on the item
    366366    @param include Options for which items that should be included/excluded from the
    367367      result, or null to include all non-removed items
  • branches/webservices/src/core/net/sf/basedb/core/RawDataTypes.java

    r3581 r3653  
    2424package net.sf.basedb.core;
    2525
     26import net.sf.basedb.core.dbengine.DbEngine;
     27import net.sf.basedb.util.Values;
    2628import net.sf.basedb.util.XMLUtil;
    2729
     30import java.util.HashSet;
    2831import java.util.List;
    2932import java.util.ArrayList;
    3033import java.util.Map;
     34import java.util.Set;
    3135import java.util.TreeMap;
    3236import java.net.URL;
     
    141145  {
    142146    List<Element> rawDataTypeTags = dom.getRootElement().getChildren("raw-data-type");
     147    DbEngine engine = HibernateUtil.getDbEngine();
     148    Set<String> usedNames = new HashSet<String>();
    143149    for (Element el : rawDataTypeTags)
    144150    {
    145       String id = el.getAttributeValue("id");
    146       String name = el.getAttributeValue("name");
    147       String description = el.getAttributeValue("description");
     151      String id = Values.getStringOrNull(el.getAttributeValue("id"));
     152      String name = Values.getStringOrNull(el.getAttributeValue("name"));
     153      String description = Values.getStringOrNull(el.getAttributeValue("description"));
    148154      String storage = el.getAttributeValue("storage");
    149       String table = el.getAttributeValue("table");
     155      String table = Values.getStringOrNull(el.getAttributeValue("table"));
    150156      int channels = XMLUtil.getIntAttribute(el, "channels", 2);
    151       List<RawDataProperty> properties = loadProperties(el);
     157     
     158      if (!ExtendedProperty.isValidName(id))
     159      {
     160        throw new InvalidDataException("Invalid id for raw data type: " + id);
     161      }
     162      if (usedNames.contains("name:" + name))
     163      {
     164        throw new InvalidDataException("Duplicate name for raw data type " +
     165          id +": name=" + name);
     166      }
     167      usedNames.add("name:" + name);
     168      if ("database".equals(storage))
     169      {
     170        if (!engine.isValidTableName(table))
     171        {
     172          throw new InvalidDataException("Invalid table for raw data type " +
     173              id +": table=" + table);
     174        }
     175        if (usedNames.contains("table:" + table))
     176        {
     177          throw new InvalidDataException("Duplicate table for raw data type " +
     178            id +": table=" + table);
     179        }
     180        usedNames.add("table:" + table);
     181      }
     182      if (channels <= 0)
     183      {
     184        throw new InvalidDataException("Number of channels must be > 0 for raw data type "+
     185            id + ": channels=" + channels);
     186      }
     187      List<RawDataProperty> properties = loadProperties(el, channels);
    152188      List<IntensityFormula> formulas = loadIntensityFormulas(el, channels);
    153189      RawDataType rdt = new RawDataType(id, name, description, channels, storage, table, properties, formulas);
     
    161197  */
    162198  @SuppressWarnings({"unchecked"})
    163   private static List<RawDataProperty> loadProperties(Element rawDataTypeElement)
     199  private static List<RawDataProperty> loadProperties(Element rawDataTypeElement, int channels)
    164200  {
    165201    List<RawDataProperty> properties = new ArrayList<RawDataProperty>();
    166202    List<Element> children = rawDataTypeElement.getChildren("property");
     203    String rawDataType = rawDataTypeElement.getAttributeValue("id");
     204    DbEngine engine = HibernateUtil.getDbEngine();
     205    Set<String> usedNames = new HashSet<String>();
    167206    for (Element property : children)
    168207    {
    169       String name = property.getAttributeValue("name");
    170       String title = property.getAttributeValue("title");
     208      String name = Values.getStringOrNull(property.getAttributeValue("name"));
     209      if (!ExtendedProperty.isValidName(name))
     210      {
     211        throw new InvalidDataException("Invalid property for raw data type " +
     212          rawDataType + ": name=" + name);
     213      }
     214      if (usedNames.contains("name:" + name))
     215      {
     216        throw new InvalidDataException("Duplicate property for raw data type " +
     217          rawDataType + ": name=" + name);
     218      }
     219      usedNames.add("name:" + name);
     220      String title = Values.getStringOrNull(property.getAttributeValue("title"));
    171221      if (title == null) title = name;
    172       String column = property.getAttributeValue("column");
    173       String description = property.getAttributeValue("description");
     222      String column = Values.getStringOrNull(property.getAttributeValue("column"));
     223      if (!engine.isValidColumnName(column))
     224      {
     225        throw new InvalidDataException("Invalid column for property " +
     226          rawDataType + "[" + name + "]: column=" + column);
     227      }
     228      if (usedNames.contains("column:" + column))
     229      {
     230        throw new InvalidDataException("Duplicate column for property " +
     231          rawDataType + "[" + name + "]: column=" + column);
     232      }
     233      usedNames.add("column:" + column);
     234      String description = Values.getStringOrNull(property.getAttributeValue("description"));
    174235      Type type = Type.fromValue(property.getAttributeValue("type"));
    175236      int length = XMLUtil.getIntAttribute(property, "length", 255);
     
    192253      }
    193254      int channel = XMLUtil.getIntAttribute(property, "channel", 0);
     255      if (channel < 0 || channel > channels)
     256      {
     257        throw new InvalidDataException("Channel for property " + rawDataType+ "[" + name + "]"
     258            +  " must be >= 0 and < " + channels + ": channel=" + channel);
     259      }
    194260      properties.add(new RawDataProperty(name, title, description, column, type, length, nullable, averageMethod, channel));
    195261    }
     
    206272    List<IntensityFormula> formulas = new ArrayList<IntensityFormula>();
    207273    List<Element> children = rawDataTypeElement.getChildren("intensity-formula");
     274    String rawDataType = rawDataTypeElement.getAttributeValue("id");
     275    Set<String> usedNames = new HashSet<String>();
    208276    for (Element formula : children)
    209277    {
    210       String name = formula.getAttributeValue("name");
    211       String title = formula.getAttributeValue("title");
     278      String name = Values.getStringOrNull(formula.getAttributeValue("name"));
     279      if (!ExtendedProperty.isValidName(name))
     280      {
     281        throw new InvalidDataException("Invalid intensity formula for raw data type " +
     282          rawDataType + ": name=" + name);
     283      }
     284      if (usedNames.contains("name:" + name))
     285      {
     286        throw new InvalidDataException("Duplicate intensity formula for raw data type " +
     287          rawDataType + ": name=" + name);
     288      }
     289      usedNames.add("name:" + name);
     290      String title = Values.getStringOrNull(formula.getAttributeValue("title"));
    212291      if (title == null) title = name;
    213       String description = formula.getAttributeValue("description");
     292      String description = Values.getStringOrNull(formula.getAttributeValue("description"));
    214293      String[] expressions = new String[channels];
    215294      for (Element expression :  (List<Element>)formula.getChildren("formula"))
    216295      {
    217296        int channel = XMLUtil.getIntAttribute(expression, "channel", 0);
     297        String exp = Values.getStringOrNull(expression.getAttributeValue("expression"));
    218298        if (channel <= 0 || channel > channels)
    219299        {
    220           throw new BaseException("Invalid channel number for expression: "+expression);
     300          throw new InvalidDataException("Channel for intensity formula " +
     301              rawDataType+ "[" + name + "]"
     302              +  " must be > 0 and < " + channels + ": channel=" + channel);
    221303        }
    222304        if (expressions[channel-1] != null)
    223305        {
    224           throw new BaseException("Expression for channel "+channel+" has already been defined: " +expression);
    225         }
    226         expressions[channel-1] = expression.getAttributeValue("expression");
     306          throw new InvalidDataException("Duplicate expression for intensity formula " +
     307            rawDataType + "[" + name + "]: channel=" + channel);
     308        }
     309        if (exp == null)
     310        {
     311          throw new InvalidDataException("Missing expression for formula " +
     312            rawDataType + "[" + name + "]: channel=" + channel);
     313        }
     314        expressions[channel-1] = exp;
    227315      }
    228316      formulas.add(new IntensityFormula(name, title, description, expressions));
  • branches/webservices/src/core/net/sf/basedb/core/Transformation.java

    r2998 r3653  
    151151  }
    152152
     153  // Keep reference to job so we can call Job.setExperiment at end of transaction
     154  private Job job;
     155 
    153156  /**
    154157    Creates a new experiment item from the given data.
     
    215218  */
    216219  /**
    217     Delete the product bioassaysets.
     220    Delete the product bioassaysets when deleting this transction.
     221    Set the experiment for the job when creating this transction.
    218222  */
    219223  void onBeforeCommit(Transactional.Action action)
     
    224228    {
    225229      deleteProducts();
     230    }
     231    else if (action == Transactional.Action.CREATE)
     232    {
     233      if (job != null)
     234      {
     235        getDbControl().refreshItem(job);
     236        job.setExperiment(getExperiment());
     237      }
    226238    }
    227239  }
     
    358370  private void setJob(Job job)
    359371  {
     372    this.job = job;
    360373    getData().setJob(job == null ? null : job.getData());
    361374  }
  • branches/webservices/src/core/net/sf/basedb/core/Type.java

    r3533 r3653  
    7070    {
    7171      if (value == null) return null;
    72       return new Integer(Float.valueOf(value).intValue());
     72      return new Integer(Double.valueOf(value).intValue());
    7373    }
    7474    public Number convertNumber(Number num)
     
    9494      throws InvalidDataException
    9595    {
    96       return new Long(Float.valueOf(value).intValue());
     96      if (value == null) return null;
     97      return new Long(Double.valueOf(value).intValue());
    9798    }
    9899    public Number convertNumber(Number num)
     
    115116      return value == null ? 0 : 4;
    116117    }
     118    public Object parseString(String value)
     119      throws InvalidDataException
     120    {
     121      if (value == null) return null;
     122      Float f = Float.valueOf(value);
     123      if (f.isNaN() || f.isInfinite()) f = null;
     124      return f;
     125    }
    117126    public Number convertNumber(Number num)
    118127    {
     
    133142    {
    134143      return value == null ? 0 : 8;
     144    }
     145    public Object parseString(String value)
     146      throws InvalidDataException
     147    {
     148      if (value == null) return null;
     149      Double d = Double.valueOf(value);
     150      if (d.isNaN() || d.isInfinite()) d = null;
     151      return d;
    135152    }
    136153    public Number convertNumber(Number num)
  • branches/webservices/src/core/net/sf/basedb/core/Update.java

    r3581 r3653  
    3131import java.util.Date;
    3232import java.util.HashMap;
     33import java.util.HashSet;
    3334import java.util.List;
    3435import java.util.Map;
     36import java.util.Set;
    3537
    3638import org.hibernate.mapping.Table;
    3739
    3840import net.sf.basedb.core.data.DataCubeData;
     41import net.sf.basedb.core.data.ExperimentData;
    3942import net.sf.basedb.core.data.FileData;
    4043import net.sf.basedb.core.data.FormulaData;
     44import net.sf.basedb.core.data.JobData;
    4145import net.sf.basedb.core.data.MeasuredBioMaterialData;
    4246import net.sf.basedb.core.data.PlateData;
    4347import net.sf.basedb.core.data.PlateMappingData;
     48import net.sf.basedb.core.data.PluginConfigurationData;
     49import net.sf.basedb.core.data.PluginDefinitionData;
    4450import net.sf.basedb.core.data.SchemaVersionData;
     51import net.sf.basedb.core.data.TransformationData;
    4552import net.sf.basedb.core.dbengine.DbEngine;
    4653import net.sf.basedb.core.dbengine.TableInfo;
     
    392399    <td>
    393400      <ul>
    394       <li>Added {@link net.sf.basedb.core.data.JobData#getDeleteJobWhenFinished()}.
    395       </ul>
    396       The update sets the <code>deleteJobWhenFinished</code> value to false for all existing jobs.
     401      <li>Added {@link net.sf.basedb.core.data.JobData#getRemoveJobWhenFinished()}.
     402      </ul>
     403      The update sets the <code>removeJobWhenFinished</code> value to false for all existing jobs.
    397404    </td>
    398405  </tr>
     
    439446    </td>
    440447  </tr>
     448
     449  <tr>
     450    <td>38</td>
     451    <td>
     452      <ul>
     453      <li>Added {@link net.sf.basedb.core.data.JobData#getExperiment()}.
     454      </ul>
     455      The update sets the experiment for jobs that belong to a single
     456      transformation.
     457    </td>
     458  </tr>
     459 
     460  <tr>
     461    <td>39</td>
     462    <td>
     463      Remove AnyToAny links created by older versions of the
     464      Base1PluginExecuter plug-in.
     465    </td>
     466  </tr>
     467 
     468  <tr>
     469    <td>40</td>
     470    <td>
     471      Change invalid property filter on 'guiContexts.itemType' to
     472      '$ctx.itemType'.
     473    </td>
     474  </tr>
    441475
    442476  </table>
     
    617651      }
    618652     
    619       if (schemaVersion < 36)
    620       {
    621         if (progress != null) progress.display((int)(35*progress_factor), "--Updating schema version: " + schemaVersion + " -> 36...");       
    622         schemaVersion = setSchemaVersionInTransaction(session, 36);
    623       }
    624      
    625      
     653      //  Schemaversion 36-37 only updates the version number
    626654      if (schemaVersion < 37)
    627655      {
     
    630658      }
    631659     
     660      if (schemaVersion < 38)
     661      {
     662        if (progress != null) progress.display((int)(37*progress_factor), "--Updating schema version: " + schemaVersion + " -> 38...");       
     663        schemaVersion = updateToSchemaVersion38(session);
     664      }
     665     
     666      if (schemaVersion < 39)
     667      {
     668        if (progress != null) progress.display((int)(38*progress_factor), "--Updating schema version: " + schemaVersion + " -> 39...");       
     669        schemaVersion = updateToSchemaVersion39(session);
     670      }
     671     
     672      if (schemaVersion < 40)
     673      {
     674        if (progress != null) progress.display((int)(39*progress_factor), "--Updating schema version: " + schemaVersion + " -> 40...");       
     675        schemaVersion = updateToSchemaVersion40(session);
     676      }
     677     
    632678      /*
    633       if (schemaVersion < 38)
    634       {
    635         if (progress != null) progress.display((int)(37*progress_factor), "--Updating schema version: " + schemaVersion + " -> 38...");
    636         schemaVersion = setSchemaVersionInTransaction(session, 38);
     679      if (schemaVersion < 41)
     680      {
     681        if (progress != null) progress.display((int)(40*progress_factor), "--Updating schema version: " + schemaVersion + " -> 41...");
     682        schemaVersion = setSchemaVersionInTransaction(session, 41);
    637683        - or -
    638         schemaVersion = updateToSchemaVersion38(session);
     684        schemaVersion = updateToSchemaVersion41(session);
    639685      }
    640686      ... etc...
     
    13861432    return schemaVersion;   
    13871433  }
     1434 
     1435  /**
     1436    Set the experiment for jobs that belong to a single transformation.
     1437    @return The new schema version (=38)
     1438  */
     1439  private static int updateToSchemaVersion38(org.hibernate.Session session)
     1440  {
     1441    final int schemaVersion = 38;
     1442    org.hibernate.Transaction tx = null;
     1443    try
     1444    {
     1445      tx = HibernateUtil.newTransaction(session);
     1446 
     1447      // Load all transformations
     1448      org.hibernate.Query query = HibernateUtil.createQuery(session,
     1449        "SELECT t FROM TransformationData t");
     1450     
     1451      List<TransformationData> transformations = HibernateUtil.loadList(TransformationData.class, query);
     1452      Map<JobData, Set<ExperimentData>> experiments = new HashMap<JobData, Set<ExperimentData>>();
     1453      for (TransformationData transformation : transformations)
     1454      {
     1455        JobData job = transformation.getJob();
     1456        if (job != null)
     1457        {
     1458          ExperimentData experiment = transformation.getExperiment();
     1459          if (!experiments.containsKey(job))
     1460          {
     1461            experiments.put(job, new HashSet<ExperimentData>());
     1462          }
     1463          experiments.get(job).add(experiment);
     1464        }
     1465      }
     1466     
     1467      for (Map.Entry<JobData, Set<ExperimentData>> entry : experiments.entrySet())
     1468      {
     1469        JobData job = entry.getKey();
     1470        Set<ExperimentData> jobExperiments = entry.getValue();
     1471        if (jobExperiments.size() == 1)
     1472        {
     1473          job.setExperiment(jobExperiments.iterator().next());
     1474        }
     1475      }
     1476     
     1477      // Update the shcema version number
     1478      setSchemaVersion(session, schemaVersion);
     1479 
     1480      // Commit the changes
     1481      HibernateUtil.commit(tx);
     1482      log.info("updateToSchemaVersion38: OK");
     1483    }
     1484    catch (BaseException ex)
     1485    {
     1486      if (tx != null) HibernateUtil.rollback(tx);
     1487      log.error("updateToSchemaVersion38: FAILED", ex);
     1488      throw ex;
     1489    }
     1490    return schemaVersion;   
     1491  }
     1492  /**
     1493    Remove AnyToAny links created by older versions of Base1PluginExecuter
     1494    @return The new schema version (=39)
     1495  */
     1496  private static int updateToSchemaVersion39(org.hibernate.Session session)
     1497  {
     1498    final int schemaVersion = 39;
     1499    org.hibernate.Transaction tx = null;
     1500    try
     1501    {
     1502      tx = HibernateUtil.newTransaction(session);
     1503 
     1504      // Load Base1PluginExecuter
     1505      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session,
     1506          "GET_PLUGINDEFINITION_FOR_CLASSNAME");
     1507      /*
     1508        SELECT pd
     1509        FROM PluginDefinitionData pd
     1510        WHERE pd.className = :className
     1511      */
     1512      query.setString("className", "net.sf.basedb.plugins.Base1PluginExecuter");
     1513      PluginDefinitionData base1Executer = HibernateUtil.loadData(PluginDefinitionData.class, query);
     1514     
     1515      // Load all plugin configurations for net.sf.basedb.plugins.Base1PluginExecuter
     1516      query = HibernateUtil.getPredefinedQuery(session,
     1517        "GET_PLUGINCONFIGURATIONS_FOR_PLUGINDEFINITION", "pc");
     1518      /*
     1519        SELECT {1}
     1520        FROM PluginConfigurationData pc
     1521        WHERE pc.pluginDefinition = :pluginDefinition
     1522      */
     1523      query.setEntity("pluginDefinition", base1Executer);
     1524      List<PluginConfigurationData> configurations =
     1525        HibernateUtil.loadList(PluginConfigurationData.class, query);
     1526
     1527      // Delete AnyToAny for each configuration
     1528      query = HibernateUtil.getPredefinedQuery(session, "DELETE_ALL_ANYTOANY_FROM");
     1529      /*
     1530        DELETE FROM AnyToAnyData ata
     1531        WHERE ata.fromId = :fromId AND ata.fromType = :fromType
     1532      */
     1533      query.setInteger("fromType", Item.PLUGINCONFIGURATION.getValue());
     1534      for (PluginConfigurationData pc : configurations)
     1535      {
     1536        query.setInteger("fromId", pc.getId());
     1537        HibernateUtil.executeUpdate(query);
     1538      }
     1539     
     1540      // Update the schema version number
     1541      setSchemaVersion(session, schemaVersion);
     1542 
     1543      // Commit the changes
     1544      HibernateUtil.commit(tx);
     1545      log.info("updateToSchemaVersion39: OK");
     1546    }
     1547    catch (BaseException ex)
     1548    {
     1549      if (tx != null) HibernateUtil.rollback(tx);
     1550      log.error("updateToSchemaVersion39: FAILED", ex);
     1551      throw ex;
     1552    }
     1553    return schemaVersion;   
     1554  }
     1555
     1556  /**
     1557    Update property filter on 'guiContexts.itemType' to '$ctx.itemType'
     1558    @return The new schema version (=40)
     1559  */
     1560  private static int updateToSchemaVersion40(org.hibernate.Session session)
     1561  {
     1562    final int schemaVersion = 40;
     1563    org.hibernate.Transaction tx = null;
     1564    try
     1565    {
     1566      tx = HibernateUtil.newTransaction(session);
     1567 
     1568      // Change property values
     1569      org.hibernate.Query query = HibernateUtil.getPredefinedSQLQuery(session,
     1570          "UPDATE_PROPERTY_FILTER");
     1571      /*
     1572        UPDATE PropertyFilters pf
     1573        SET pf.property = :newProperty
     1574        WHERE pf.property = :oldProperty
     1575       */
     1576      query.setString("oldProperty", "guiContexts.itemType");
     1577      query.setString("newProperty", "$ctx.itemType");
     1578      HibernateUtil.executeUpdate(query);
     1579
     1580      // Update the schema version number
     1581      setSchemaVersion(session, schemaVersion);
     1582 
     1583      // Commit the changes
     1584      HibernateUtil.commit(tx);
     1585      log.info("updateToSchemaVersion40: OK");
     1586    }
     1587    catch (BaseException ex)
     1588    {
     1589      if (tx != null) HibernateUtil.rollback(tx);
     1590      log.error("updateToSchemaVersion40: FAILED", ex);
     1591      throw ex;
     1592    }
     1593    return schemaVersion;   
     1594  }
     1595
    13881596 
    13891597  /**
  • branches/webservices/src/core/net/sf/basedb/core/data/ExperimentData.java

    r2962 r3653  
    313313    this.transformations = transformations;
    314314  }
     315 
     316  private Set<JobData> jobs;
     317  /**
     318    This is the inverse end.
     319    @see JobData#getExperiment()
     320    @since 2.4
     321    @hibernate.set lazy="true" inverse="true" cascade="delete"
     322    @hibernate.collection-key column="`experiment_id`"
     323    @hibernate.collection-one-to-many class="net.sf.basedb.core.data.JobData"
     324  */
     325  Set<JobData> getJobs()
     326  {
     327    return jobs;
     328  }
     329  void setJobs(Set<JobData> jobs)
     330  {
     331    this.jobs = jobs;
     332  }
    315333
    316334  private Set<AnnotationTypeData> experimentalFactors;
  • branches/webservices/src/core/net/sf/basedb/core/data/ExtendableData.java

    r3581 r3653  
    6868    <td>
    6969      The property name of the extended property.
    70       See {@link net.sf.basedb.core.ExtendedProperty#getName()}.
     70      See {@link net.sf.basedb.core.ExtendedProperty#getName()}. The name
     71      must only contain letters, numbers and underscores but the first character
     72      can't be a number. The name must be unique within the class.
    7173    </td>
    7274  </tr>
     
    8991    <td>
    9092      The database column name of the extended property. This value
    91       must of course be unique for each class.
    92       See {@link net.sf.basedb.core.ExtendedProperty#getColumn()}.
     93      must be unique for each class. The value is validated by the
     94      {@link net.sf.basedb.core.dbengine.DbEngine#isValidColumnName(String)}
     95      which normally means it must follow the same rules as the <code>name</code>
     96      attribute. See {@link net.sf.basedb.core.ExtendedProperty#getColumn()}.
    9397    </td>
    9498  </tr>
  • branches/webservices/src/core/net/sf/basedb/core/data/JobData.java

    r3533 r3653  
    128128  }
    129129
     130  private ExperimentData experiment;
     131 
     132  /**
     133    The experiment this job is a part of.
     134    @since 2.4
     135    @hibernate.many-to-one column="`experiment_id`" not-null="false" outer-join="false"
     136  */
     137  public ExperimentData getExperiment()
     138  {
     139    return experiment;
     140  }
     141  public void setExperiment(ExperimentData experiment)
     142  {
     143    this.experiment = experiment;
     144  }
     145 
    130146  private int parameterVersion;
    131147  /**
  • branches/webservices/src/core/net/sf/basedb/core/dbengine/AbstractDbEngine.java

    r2812 r3653  
    2424package net.sf.basedb.core.dbengine;
    2525
     26import java.util.regex.Pattern;
     27
    2628/**
    2729  An abstract superclass with default implementations for most {@link DbEngine}
     
    3638{
    3739
     40  /**
     41    A regexp checking for invalid characters.
     42  */
     43  private static final Pattern valid = Pattern.compile("[a-zA-Z_][a-zA-Z0-9_]*");
     44 
    3845  /**
    3946    Create AbstractDbEngine.
     
    121128    return "EXP("+ value + ")";
    122129  }
     130  /**
     131    Checks that the name only contains the following characters: a-zA-Z0-9_
     132    It must also start with a letter or underscore.
     133    @since 2.4
     134  */
     135  public boolean isValidTableName(String tableName)
     136  {
     137    return isValidName(tableName);
     138  }
     139 
     140  /**
     141    Checks that the name only contains the following characters: a-zA-Z0-9_
     142    It must also start with a letter or underscore.
     143  */
     144  public boolean isValidColumnName(String columnName)
     145  {
     146    return isValidName(columnName);
     147  }
    123148  // -------------------------------------------
    124149
     150  /**
     151    Check that the name only contains a-zA-Z0-9_ and starts with
     152    a letter or underscore.
     153    @since 2.4
     154  */
     155  protected boolean isValidName(String name)
     156  {
     157    return name == null ? false : valid.matcher(name).matches();
     158  }
     159 
     160 
    125161}
  • branches/webservices/src/core/net/sf/basedb/core/dbengine/DbEngine.java

    r3533 r3653  
    239239  public String exp(String value);
    240240
     241  /**
     242    Check if a given string is valid to be used as a table name in the
     243    current database.
     244    @param tableName The string to check
     245    @return TRUE if the name is valid, FALSE if not
     246    @since 2.4
     247  */
     248  public boolean isValidTableName(String tableName);
     249 
     250  /**
     251    Check if a given string is valid to be used as a column name in the
     252    current database.
     253    @param columnName The string to check
     254    @return TRUE if the name is valid, FALSE if not
     255    @since 2.4
     256  */
     257  public boolean isValidColumnName(String columnName);
    241258}
  • branches/webservices/src/core/net/sf/basedb/core/dtd/extended-properties.dtd

    • Property svn:keyword set to Id Date
  • branches/webservices/src/core/net/sf/basedb/core/dtd/helpfile.dtd

    • Property svn:eol-style set to native
    • Property svn:keyword set to Id Date
  • branches/webservices/src/core/net/sf/basedb/core/dtd/plugin-configuration-file.dtd

    • Property svn:eol-style set to native
    • Property svn:keyword set to Id Date
  • branches/webservices/src/core/net/sf/basedb/core/dtd/predefined-queries.dtd

    • Property svn:keyword set to Id Date
  • branches/webservices/src/core/net/sf/basedb/core/dtd/presets.dtd

    • Property svn:eol-style set to native
    • Property svn:keyword set to Id Date
  • branches/webservices/src/core/net/sf/basedb/core/dtd/raw-data-types.dtd

    • Property svn:keyword set to Id Date
  • branches/webservices/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java

    r3581 r3653  
    3131import net.sf.basedb.core.BioAssaySet;
    3232import net.sf.basedb.core.DbControl;
     33import net.sf.basedb.core.DynamicSpotQuery;
    3334import net.sf.basedb.core.Experiment;
    3435import net.sf.basedb.core.Item;
     
    4041import net.sf.basedb.core.StringParameterType;
    4142import net.sf.basedb.core.Transformation;
     43import net.sf.basedb.core.VirtualColumn;
     44import net.sf.basedb.core.query.Dynamic;
     45import net.sf.basedb.core.query.Expression;
     46import net.sf.basedb.core.query.Expressions;
     47import net.sf.basedb.core.query.Restrictions;
    4248
    4349/**
     
    111117    The bioAssays subset parameter.
    112118    To use when working on subset of bioassays in a bioAssaySet
    113     @see #getSourceBioAssaysSubSetParameter(String, String, List<BioAssay>)
     119    @see #getSourceBioAssaysParameter(String, String)
    114120   */
    115121  private PluginParameter<BioAssay> sourceSubSetParameter = null;
     
    211217  }
    212218 
    213   protected static final String SOURCE_BIOASSAYS = "source_subset";
     219  protected static final String SOURCE_BIOASSAYS = "bioAssays";
    214220 
    215221  /**
     
    217223    for the plugin.
    218224      @param label The parameter's label. Uses a default value if null.
    219    * @param description Description of the parameter. Uses a default value if null.
     225      @param description Description of the parameter. Uses a default value if null.
    220226    @return A plugin parameter
    221227    @since 2.4
     
    414420  }
    415421
    416  
     422  /**
     423    Restricts a query to only include values from listed bioassays
     424      @param query The query to set restriction on
     425      @param bioAssays A list with bioassays the restriction should include
     426      @return A DynamicSpotQuery object. The query parameter is restricted if bioAssays holds item(s),
     427        otherwise it will it will be the same
     428      @since 2.4
     429  */
     430  protected DynamicSpotQuery restrictSource(DynamicSpotQuery query, List<BioAssay> bioAssays)
     431  {
     432    if ( (bioAssays != null) && !bioAssays.isEmpty() )
     433    {
     434      Expression[] selectedColumns = new Expression[bioAssays.size()];
     435      for (int i=0; i<selectedColumns.length; i++)
     436      {
     437        BioAssay ba = bioAssays.get(i);
     438        selectedColumns[i] = Expressions.integer(ba.getDataCubeColumnNo());
     439      }       
     440      query.restrict(Restrictions.in(
     441          Dynamic.column(VirtualColumn.COLUMN),
     442          selectedColumns));
     443    }
     444    return query;
     445  }
    417446}
  • branches/webservices/src/core/net/sf/basedb/core/plugin/AbstractExporterPlugin.java

    r3133 r3653  
    7474 
    7575  protected static final BooleanParameterType overwriteType =
    76     new BooleanParameterType(false, false);
     76    new BooleanParameterType(null, false);
    7777 
    7878  /**
  • branches/webservices/src/core/net/sf/basedb/core/plugin/ExportOutputStream.java

    r2981 r3653  
    8888    out.write(b);
    8989  }
     90  @Override
    9091  public void write(int b)
    9192    throws IOException
  • branches/webservices/src/core/net/sf/basedb/util/FileUtil.java

    r3533 r3653  
    8686        totalBytes += bytes;
    8787        out.write(buffer, 0, bytes);
     88      }
     89    }
     90    return totalBytes;
     91  }
     92 
     93  /**
     94    Read from the input stream until the end is reached.
     95   
     96    @param in The <code>InputStream</code> to read from
     97    @return The number of bytes copied
     98    @throws IOException This exception is thrown if there is an error
     99    @since 2.4
     100  */
     101  public static long read(InputStream in)
     102    throws IOException
     103  {
     104    int bytes = 0;
     105    long totalBytes = 0;
     106    byte[] buffer = new byte[BUFFER_SIZE];
     107 
     108    while (bytes != -1) // -1 = end of stream
     109    {
     110      bytes = in.read(buffer, 0, buffer.length);
     111      if (bytes > 0)
     112      {
     113        totalBytes += bytes;
    88114      }
    89115    }
  • branches/webservices/src/core/net/sf/basedb/util/InputStreamSplitter.java

    r2689 r3653  
    4343{
    4444
     45  private int numRead;
     46 
    4547  /**
    4648    The source input stream to read from.
     
    5456 
    5557  /**
    56     Since the various read methods call each other we must keep
    57     track of this so only the first called method copies the data.
    58   */
    59   private boolean doCopy = true;
    60  
    61   /**
    62     Create a new input stream splitter.
     58    If the {@link #skip(long)} method should copy
     59    to the output streams or no.
     60  */
     61  private final boolean copySkipped;
     62 
     63  /**
     64    If the remainder of the input stream should be copied
     65    if it is closed before the end.
     66  */
     67  private final boolean readToEnd;
     68 
     69  /**
     70    Create a new input stream splitter. Skipped bytes are not copied
     71    and the remainder of the stream is not copied if closed.
    6372    @param in The input stream to read from
    6473    @param copyTo The output streams to copy data to
    6574  */
    6675  public InputStreamSplitter(InputStream in, OutputStream... copyTo)
     76  {
     77    this(in, false, false, copyTo);
     78  }
     79
     80  /**
     81    Create a new input stream splitter. Skipped bytes are not copied
     82    and the remainder of the stream is not copied if closed.
     83    @param in The input stream to read from
     84    @param copyTo The output streams to copy data to
     85    @since 2.4
     86  */
     87  public InputStreamSplitter(InputStream in, boolean copySkipped, boolean readToEnd, OutputStream... copyTo)
    6788  {
    6889    if (in == null) throw new NullPointerException("in");
     
    7091    this.in = in;
    7192    this.copyTo = copyTo;
    72   }
     93    this.copySkipped = copySkipped;
     94    this.readToEnd = readToEnd;
     95  }
     96 
    7397  /*
    7498    From the InputStream class
     
    85109    throws IOException
    86110  {
     111    if (readToEnd)
     112    {
     113      FileUtil.read(this);
     114    }
    87115    in.close();
     116    for (OutputStream out : copyTo)
     117    {
     118      out.flush();
     119    }
    88120  }
    89121  @Override
    90122  public synchronized void mark(int readlimit)
    91   {
    92     in.mark(readlimit);
    93   }
     123  {}
    94124  @Override
    95125  public boolean markSupported()
    96126  {
    97     return in.markSupported();
    98   }
     127    return false;
     128  }
     129  @Override
    99130  public int read()
    100131    throws IOException
    101132  {
    102     boolean oldDoCopy = doCopy;
    103     doCopy = false;
    104133    int result = in.read();
    105     doCopy = oldDoCopy;
    106     if (doCopy && result != -1) copy(result);
     134    if (result >= 0)
     135    {
     136      ++numRead;
     137      copy(result);
     138    }
    107139    return result;
    108140  }
     
    111143    throws IOException
    112144  {
    113     boolean oldDoCopy = doCopy;
    114     doCopy = false;
    115145    int result = in.read(b, off, len);
    116     doCopy = oldDoCopy;
    117     if (doCopy && result > 0) copy(b, off, result);
     146    if (result > 0)
     147    {
     148      numRead += result;
     149      copy(b, off, result);
     150    }
    118151    return result;
    119152  }
     
    128161    throws IOException
    129162  {
    130     in.reset();
     163    throw new IOException("reset/mark is not supported");
    131164  }
    132165  @Override
     
    134167    throws IOException
    135168  {
    136     boolean oldDoCopy = doCopy;
    137     doCopy = false;
    138     long result = in.skip(n);
    139     doCopy = oldDoCopy;
     169    long result = 0;
     170    if (copySkipped)
     171    {
     172      // This will call the read(byte[], int, int) method
     173      result = super.skip(n);
     174    }
     175    else
     176    {
     177      in.skip(n);
     178    }
    140179    return result;
    141180  }
     
    143182
    144183  /**
     184    Get the number of bytes that has been read or skipped
     185    from the input stream.
     186    @since 2.4
     187  */
     188  public long getNumRead()
     189  {
     190    return numRead;
     191  }
     192 
     193  /**
    145194    Write data to all output streams.
    146195  */
  • branches/webservices/src/core/net/sf/basedb/util/JarClassLoader.java

    r3533 r3653  
    6868    A map of all loaded class loaders.
    6969  */
    70   private static final HashMap<String, ClassLoader> classLoaders = new HashMap<String, ClassLoader>();
     70  private static final HashMap<String, JarClassLoader> classLoaders =
     71    new HashMap<String, JarClassLoader>();
    7172
    7273  /**
     
    8283    throws IOException
    8384  {
    84     ClassLoader cl = classLoaders.get(jarPath);
     85    return getInstance(jarPath, false);
     86  }
     87
     88  /**
     89    Get a class loader for the specified JAR file, optionally unloading an the old
     90    one if the JAR file has been modified. A new class loader is created if no
     91    class loader exists or if <code>autoUnload</code> is <code>true</code> and the JAR file
     92    has changed since the existing class loader was created.
     93   
     94    @param jarPath The path to a JAR file
     95    @param autoUnload If TRUE the old class loaded will automaticall be unloaded if the
     96      JAR file has been modified (if the timestamp and/or size) is different
     97    @return A class loader
     98    @throws IOException If the jar file can't be loaded
     99    @since 2.4
     100  */
     101  public static final ClassLoader getInstance(String jarPath, boolean autoUnload)
     102    throws IOException
     103  {
     104    JarClassLoader cl = classLoaders.get(jarPath);
     105    if (cl != null && autoUnload)
     106    {
     107      // Check if JAR file exists and has same timestamp and size
     108      File jarFile = new File(jarPath);
     109      boolean isSame = jarFile.exists() && jarFile.lastModified() == cl.jarTimeStamp && jarFile.length() == cl.jarTimeStamp;
     110      if (!isSame) cl = null;
     111    }
    85112    if (cl == null)
    86113    {
     
    93120    return cl;
    94121  }
    95 
     122 
     123 
    96124  /**
    97125    Unload the class loader for the given JAR file. The class loader will
     
    134162 
    135163  /**
     164    The timestamp of the JAR file.
     165  */
     166  private final long jarTimeStamp;
     167 
     168  /**
     169    The size of the JAR file.
     170  */
     171  private final long jarSize;
     172 
     173 
     174  /**
    136175    Create a new JAR file class loader.
    137176    @param jarPath The path to the JAR file
     
    145184    mainJarFile = new File(jarPath);
    146185    if (!mainJarFile.exists()) throw new InvalidDataException("JAR file not found: " + jarPath);
     186    this.jarTimeStamp = mainJarFile.lastModified();
     187    this.jarSize = mainJarFile.length();
    147188    classPath = new HashMap<String, File>();
    148189    loadJarFile(mainJarFile, true);
  • branches/webservices/src/core/net/sf/basedb/util/RemovableUtil.java

    r3133 r3653  
    167167    Sets the removed-flag for all subitems to a parent
    168168    @param dc The <code>DbControl</code> wich will be used for database access
    169     @param parent Parent of the subitems that shall be removed
     169    @param item Parent of the subitems that shall be removed
    170170    @param removed True if the subitems should be flagged removed.
    171171        False if the subitems should be restored
  • branches/webservices/src/core/net/sf/basedb/util/Values.java

    r3194 r3653  
    6565    if (value != null)
    6666    {
    67       try { return Float.valueOf(value).intValue(); }
     67      try { return Double.valueOf(value).intValue(); }
    6868      catch (Throwable t) {}
    6969    }
     
    7575    if (value != null)
    7676    {
    77       try { return Float.valueOf(value).intValue(); }
     77      try { return Double.valueOf(value).intValue(); }
    7878      catch (Throwable t) {}
    7979    }
  • branches/webservices/src/core/net/sf/basedb/util/XMLUtil.java

    r2304 r3653  
    9191 
    9292  /**
    93     Validate an <code>InputStream</code> against a DTD file
    94     and return it as a <code>Document</code>
    95    
    96     @param is The inputstream to the XML
    97     @param dtdFile The URL to the DTD used for validation
    98     @return A <code>Document</code> object
     93    @deprecated Use {@link #getValidatedXML(InputStream, URL, String)} instead
    9994  */
    10095  public static Document getValidatedXML(InputStream is, URL dtdFile)
    10196      throws JDOMException, IOException
    10297  {
    103     SAXBuilder sax = new SAXBuilder(xmlParserClass, true);
    104     Validator validator = new Validator(null, dtdFile);
    105     // The entity resolver lets us find the correct DTD for validating
    106     sax.setEntityResolver(validator);
    107     // So we can throw our own exception messages if there is a parse error
    108     sax.setErrorHandler(validator);
    109     Document dom = sax.build(is);
    110     is.close();
    111     return dom;
     98    return getValidatedXML(is, dtdFile, null);
    11299  }
    113100 
     
    127114  {   
    128115    InputStream is = xmlFile.openStream();   
    129     Document xmlDoc = getValidatedXML(is, dtdFile);
     116    Document xmlDoc = getValidatedXML(is, dtdFile, xmlFile.toString());
    130117    return xmlDoc;
    131118  }
     
    157144
    158145  /**
     146    Validate an <code>InputStream</code> against a DTD file
     147    and return it as a <code>Document</code>
     148   
     149    @param is The inputstream to the XML
     150    @param dtdFile The URL to the DTD used for validation
     151    @param filename The filename of the original XML data, used for error reporting only;
     152      use null if the filename is not known
     153    @return A <code>Document</code> object
     154    @since 2.4
     155  */
     156  public static Document getValidatedXML(InputStream is, URL dtdFile, String filename)
     157      throws JDOMException, IOException
     158  {
     159    SAXBuilder sax = new SAXBuilder(xmlParserClass, true);
     160    Validator validator = new Validator(filename, dtdFile);
     161    // The entity resolver lets us find the correct DTD for validating
     162    sax.setEntityResolver(validator);
     163    // So we can throw our own exception messages if there is a parse error
     164    sax.setErrorHandler(validator);
     165    Document dom = sax.build(is);
     166    is.close();
     167    return dom;
     168  }
     169 
     170 
     171  /**
    159172    Get the value of an attribute as an integer. If the attribute is missing or
    160173    doesn't contain an integer, the default value is returned.
  • branches/webservices/src/core/net/sf/basedb/util/jep/Jep.java

    r3533 r3653  
    2424package net.sf.basedb.util.jep;
    2525
     26import java.util.Collection;
    2627import java.util.Vector;
    2728
     
    3435import net.sf.basedb.core.query.Restriction;
    3536import net.sf.basedb.util.Enumeration;
     37import net.sf.basedb.util.jep.convert.ConverterFactory;
     38import net.sf.basedb.util.jep.convert.JepConversionFunction;
    3639
    3740import org.nfunk.jep.JEP;
    3841import org.nfunk.jep.Node;
    39 import org.nfunk.jep.ASTFunNode;
    4042import org.nfunk.jep.ASTVarNode;
    4143import org.nfunk.jep.ASTConstant;
    42 import org.nfunk.jep.OperatorSet;
    43 import org.nfunk.jep.Operator;
    44 import org.nfunk.jep.function.Abs;
    45 import org.nfunk.jep.function.Exp;
    46 import org.nfunk.jep.function.PostfixMathCommandI;
    47 import org.nfunk.jep.function.SquareRoot;
    48 import org.nfunk.jep.function.Subtract;
    49 import org.nfunk.jep.function.Add;
    50 import org.nfunk.jep.function.Divide;
    51 import org.nfunk.jep.function.Multiply;
    52 import org.nfunk.jep.function.UMinus;
    53 import org.nfunk.jep.function.Logarithm;
    54 import org.nfunk.jep.function.NaturalLogarithm;
    55 import org.nfunk.jep.function.Comparative;
    56 import org.nfunk.jep.function.Logical;
    57 import org.nfunk.jep.function.Not;
    5844
    5945/**
     
    8672
    8773  private static Enumeration<String, String> functions;
     74  private static Enumeration<String, String> operators;
    8875 
    8976  /**
     
    125112 
    126113  /**
    127     Get a list of functions supported by the {@link #jepToExpression(JEP)}
    128     converter.
     114    Get a list of built-in functions supported by the {@link #jepToExpression(JEP)}
     115    converter. More functions can be registered when creating the JEP
     116    expression (see {@link #newJep(String, JepFunction[])}).
     117   
    129118    @return An enumeration with the name of the function in the key
    130119      and a description in the value part
     
    135124    {
    136125      functions = new Enumeration<String, String>();
    137       functions.add("log", "10-based logarithm");
     126      // Built-in converters
     127      Collection<JepConversionFunction<?>> converters = ConverterFactory.getConverters();
     128      for (JepConversionFunction converter : converters)
     129      {
     130        if (converter.isFunction())
     131        {
     132          functions.add(converter.getName(), converter.getDescription());
     133        }
     134      }
     135      // Other standard functions that we always add; see newJep() method
    138136      functions.add("log2", "2-based logarithm");
    139       functions.add("ln", "Natural logarithm");
    140       functions.add("exp", "Exponential");
    141       functions.add("sqrt", "Square root");
    142       functions.add("abs", "Absolute value");
     137      functions.sortKeys();
    143138      functions.lock();
    144139    }
    145140    return functions;
    146141  }
     142 
     143  /**
     144    Get a list of built-in operators supported by the {@link #jepToExpression(JEP)}
     145    and {@link #jepToRestriction(JEP)} converter. It is not possible to
     146    register more operators.
     147   
     148    @return An enumeration with the symbol of the operator in the key
     149      and a description in the value part
     150    @since 2.4
     151  */
     152  public static Enumeration<String, String> getOperators()
     153  {
     154    if (operators == null)
     155    {
     156      operators = new Enumeration<String, String>();
     157      // Built-in converters
     158      Collection<JepConversionFunction<?>> converters = ConverterFactory.getConverters();
     159      for (JepConversionFunction converter : converters)
     160      {
     161        if (converter.isOperator())
     162        {
     163          operators.add(converter.getName(), converter.getDescription());
     164        }
     165      }
     166      operators.sortKeys();
     167      operators.lock();
     168    }
     169    return operators;
     170  }
     171
    147172 
    148173  /**
     
    228253    throws BaseException
    229254  {
    230     return nodeToRestriction(jep.getTopNode(), jep.getOperatorSet());
     255    return nodeToRestriction(jep.getTopNode());
    231256  }
    232257 
     
    245270    Convert a node with it's children to an expression.
    246271  */
     272  @SuppressWarnings("unchecked")
    247273  public static Expression nodeToExpression(Node node)
    248274    throws BaseException
    249275  {
    250     int numChildren = node.jjtGetNumChildren();
    251     if (node instanceof ASTFunNode)
    252     {
    253       ASTFunNode funNode = (ASTFunNode)node;
    254       PostfixMathCommandI function = funNode.getPFMC();
    255       if (function instanceof Add)
    256       {
    257         if (numChildren != 2)
    258         {
    259           throw new BaseException("Invalid number of expressions for add function: " + numChildren);
    260         }
    261         return Expressions.add(
    262           nodeToExpression(node.jjtGetChild(0)),
    263           nodeToExpression(node.jjtGetChild(1))
    264         );
    265       }
    266       else if (function instanceof Subtract)
    267       {
    268         if (numChildren != 2)
    269         {
    270           throw new BaseException("Invalid number of expressions for subtract function: " + numChildren);
    271         }
    272         return Expressions.subtract(
    273           nodeToExpression(node.jjtGetChild(0)),
    274           nodeToExpression(node.jjtGetChild(1))
    275         );
    276       }
    277       else if (function instanceof Multiply)
    278       {
    279         if (numChildren != 2)
    280         {
    281           throw new BaseException("Invalid number of expressions for multiply function: " + numChildren);
    282         }
    283         return Expressions.multiply(
    284           nodeToExpression(node.jjtGetChild(0)),
    285           nodeToExpression(node.jjtGetChild(1))
    286         );
    287       }
    288       else if (function instanceof Divide)
    289       {
    290         if (numChildren != 2)
    291         {
    292           throw new BaseException("Invalid number of expressions for divide function: " + numChildren);
    293         }
    294         return Expressions.divide(
    295           nodeToExpression(node.jjtGetChild(0)),
    296           nodeToExpression(node.jjtGetChild(1))
    297         );
    298       }
    299       else if (function instanceof UMinus)
    300       {
    301         if (numChildren != 1)
    302         {
    303           throw new BaseException("Invalid number of expressions for negate function: " + numChildren);
    304         }
    305         return Expressions.negate(nodeToExpression(node.jjtGetChild(0)));
    306       }
    307       else if (function instanceof Logarithm)
    308       {
    309         if (numChildren != 1)
    310         {
    311           throw new BaseException("Invalid number of expressions for 'log10' function: " + numChildren);
    312         }
    313         return Expressions.log10(nodeToExpression(node.jjtGetChild(0)));
    314       }
    315       else if (function instanceof NaturalLogarithm)
    316       {
    317         if (numChildren != 1)
    318         {
    319           throw new BaseException("Invalid number of expressions for 'ln' function: " + numChildren);
    320         }
    321         return Expressions.ln(nodeToExpression(node.jjtGetChild(0)));
    322       }
    323       else if (function instanceof SquareRoot)
    324       {
    325         if (numChildren != 1)
    326         {
    327           throw new BaseException("Invalid number of expressions for 'sqrt' function: " + numChildren);
    328         }
    329         return Expressions.sqrt(nodeToExpression(node.jjtGetChild(0)));
    330       }
    331       else if (function instanceof Abs)
    332       {
    333         if (numChildren != 1)
    334         {
    335           throw new BaseException("Invalid number of expressions for 'sqrt' function: " + numChildren);
    336         }
    337         return Expressions.abs(nodeToExpression(node.jjtGetChild(0)));
    338       }
    339       else if (function instanceof Exp)
    340       {
    341         if (numChildren != 1)
    342         {
    343           throw new BaseException("Invalid number of expressions for 'sqrt' function: " + numChildren);
    344         }
    345         return Expressions.exp(nodeToExpression(node.jjtGetChild(0)));
    346       }
    347       else if (function instanceof JepExpressionFunction)
    348       {
    349         return ((JepExpressionFunction)function).toExpression(node);
    350       }
    351       else
    352       {
    353         throw new BaseException("Unsupported JEP function: " + node);
    354       }
    355     }
    356     else if (node instanceof ASTVarNode)
    357     {
    358       ASTVarNode varNode = (ASTVarNode)node;
    359       String name = varNode.getName();
    360       if ("NULL".equalsIgnoreCase(name)) name = null;
    361       return name == null ? null : Expressions.parameter(name);
    362     }
    363     else if (node instanceof ASTConstant)
    364     {
    365       ASTConstant constNode = (ASTConstant)node;
    366       Object value = constNode.getValue();
    367       if (value instanceof Integer)
    368       {
    369         return Expressions.integer((Integer)value);
    370       }
    371       else if (value instanceof Float)
    372       {
    373         return Expressions.aFloat((Float)value);
    374       }
    375       else if (value instanceof Double)
    376       {
    377         return Expressions.aFloat(((Double)value).floatValue());
    378       }
    379       else if (value instanceof String)
    380       {
    381         return Expressions.string((String)value);
    382       }
    383       else
    384       {
    385         throw new BaseException("Unsupported type of constant: " + value.getClass().getName());
    386       }
     276    JepConversionFunction converter = ConverterFactory.getConverterByClass(node);
     277    Expression e = null;
     278    if (converter != null)
     279    {
     280      e = converter.toExpression(node);
    387281    }
    388282    else
    389283    {
    390       throw new BaseException("Unknown JEP node: " + node);
    391     }
    392   }
    393  
    394   private static Restriction nodeToRestriction(Node node, OperatorSet opSet)
    395     throws BaseException
    396   {
    397     int numChildren = node.jjtGetNumChildren();
    398     if (node instanceof ASTFunNode)
    399     {
    400       ASTFunNode funNode = (ASTFunNode)node;
    401       PostfixMathCommandI function = funNode.getPFMC();
    402       if (function instanceof Comparative || function instanceof Logical)
    403       {
    404         Operator op = funNode.getOperator();
    405         if (numChildren != 2)
    406         {
    407           throw new BaseException("Invalid number of expressions for '"+ op.getSymbol()+"' function: " + numChildren);
    408         }
    409         if (op == opSet.getEQ())
    410         {
    411           // A == B
    412           return Restrictions.eq(
    413             nodeToExpression(node.jjtGetChild(0)),
    414             nodeToExpression(node.jjtGetChild(1))
    415           );
    416         }
    417         else if (op == opSet.getNE())
    418         {
    419           // A <> B
    420           return Restrictions.neq(
    421             nodeToExpression(node.jjtGetChild(0)),
    422             nodeToExpression(node.jjtGetChild(1))
    423           );
    424         }
    425         else if (op == opSet.getLT())
    426         {
    427           // A < B
    428           return Restrictions.lt(
    429             nodeToExpression(node.jjtGetChild(0)),
    430             nodeToExpression(node.jjtGetChild(1))
    431           );
    432         }
    433         else if (op == opSet.getLE())
    434         {
    435           // A <= B
    436           return Restrictions.lteq(
    437             nodeToExpression(node.jjtGetChild(0)),
    438             nodeToExpression(node.jjtGetChild(1))
    439           );
    440         }
    441         else if (op == opSet.getGT())
    442         {
    443           // A > B
    444           return Restrictions.gt(
    445             nodeToExpression(node.jjtGetChild(0)),
    446             nodeToExpression(node.jjtGetChild(1))
    447           );
    448         }
    449         else if (op == opSet.getGE())
    450         {
    451           // A >= B
    452           return Restrictions.gteq(
    453             nodeToExpression(node.jjtGetChild(0)),
    454             nodeToExpression(node.jjtGetChild(1))
    455           );
    456         }
    457         else if (op == opSet.getAnd())
    458         {
    459           // A AND B
    460           return Restrictions.and(
    461             nodeToRestriction(node.jjtGetChild(0), opSet),
    462             nodeToRestriction(node.jjtGetChild(1), opSet)
    463           );
    464         }
    465         else if (op == opSet.getOr())
    466         {
    467           // A OR B
    468           return Restrictions.or(
    469             nodeToRestriction(node.jjtGetChild(0), opSet),
    470             nodeToRestriction(node.jjtGetChild(1), opSet)
    471           );
    472         }
    473         else
    474         {
    475           throw new BaseException("Unsupported operator: "+ op.getSymbol());
    476         }
    477       }
    478       else if (function instanceof Not)
    479       {
    480         if (numChildren != 1)
    481         {
    482           throw new BaseException("Invalid number of expressions for not function: " + numChildren);
    483         }
    484         return Restrictions.not(nodeToRestriction(node.jjtGetChild(0), opSet));
    485       }
    486       else if (function instanceof JepRestrictionFunction)
    487       {
    488         return ((JepRestrictionFunction)function).toRestriction(node);
    489       }
    490       else
    491       {
    492         throw new BaseException("Unsupported JEP function: " + node);
    493       }
     284      throw new BaseException("Unsupported JEP function: " + node);
     285    }
     286    return e;
     287  }
     288 
     289  /**
     290    Convert a node with it's children to a restriction.
     291    @since 2.4
     292  */
     293  @SuppressWarnings("unchecked")
     294  public static Restriction nodeToRestriction(Node node)
     295    throws BaseException
     296  {
     297    JepConversionFunction converter = ConverterFactory.getConverterByClass(node);
     298    Restriction r = null;
     299    if (converter != null)
     300    {
     301      r = converter.toRestriction(node);
    494302    }
    495303    else
    496304    {
    497       throw new BaseException("Unknown JEP node: " + node);
    498     }
     305      throw new BaseException("Unsupported JEP function: " + node);
     306    }
     307    return r;
    499308  }
    500309 
  • branches/webservices/src/core/net/sf/basedb/util/jep/PositionFunction.java

    r2992 r3653  
    3838  JEP expression parser. The function will look up position.
    3939  For example:
    40   <code>pos</code>
     40  <code>pos()</code>
    4141  <p>
    4242  To be able to use this function it must be registered with the JEP
    43   parser and, before the expression is evaluated, a {@link SqlResult} object must be set.
     43  parser. This function can only be used to convert a JEP expression to
     44  a Query API {@link Expression}. It doesn't support dynamic evalution.
    4445 
    4546  @author Enell
     
    4748  @base.modified $Date$
    4849  @see Jep
    49   @see BioAssaySetUtil#createJepExpression(DbControl, BioAssaySet, String)
     50  @see net.sf.basedb.util.BioAssaySetUtil#createJepExpression(net.sf.basedb.core.DbControl, net.sf.basedb.core.BioAssaySet, String, boolean)
    5051*/
    51 public class PositionFunction implements JepExpressionFunction
     52public class PositionFunction
     53  implements JepExpressionFunction
    5254{
    5355
     
    9294    Can't be changed.
    9395  */
    94   public void setCurNumberOfParameters(int n) {}
     96  public void setCurNumberOfParameters(int n)
     97  {}
     98 
    9599  public boolean checkNumberOfParameters(int n)
    96100  {
  • branches/webservices/src/core/net/sf/basedb/util/overview/ExperimentOverview.java

    r3533 r3653  
    885885    Add a labeled extract child node to the labeled extracts folder. Creates an
    886886    item-type subnode with the name <code>labeledextract.ID</code> where ID is the ID of the
    887     {@link LabledExtract}.
     887    {@link LabeledExtract}.
    888888  */
    889889  private Node addLabeledExtract(DbControl dc, Node parentNode, LabeledExtract le)
  • branches/webservices/src/core/net/sf/basedb/util/overview/ValidationOptions.java

    r3133 r3653  
    107107    @param clearFirst If the current settings should be cleared
    108108      before the new ones are loaded from the preset
    109     @see #saveToPreset(Preset)
     109    @see #saveToPreset(net.sf.basedb.core.Presets.Preset)
    110110  */
    111111  public void loadFromPreset(Preset preset, boolean clearFirst)
     
    122122    is used as key and the {@link Severity#name()} is used as value.
    123123    @param preset The preset to save the settings to
    124     @see #loadFromPreset(Preset, boolean)
    125124  */
    126   public void saveToPreset(Preset preset)
     125  public void saveToPreset(net.sf.basedb.core.Presets.Preset preset)
    127126  {
    128127    for (Map.Entry<String, Severity> entry : options.entrySet())
  • branches/webservices/src/core/net/sf/basedb/util/parser/ColFunction.java

    r3133 r3653  
    4444  <pre class="code">
    4545FlatFileParser ffp = ...
    46 Mapper diameterMapper = ffp.getMapper("col('Radius') * 2");
     46Mapper diameterMapper = ffp.getMapper("=col('Radius') * 2");
    4747while (ffp.hasMoreData())
    4848{
  • branches/webservices/src/core/net/sf/basedb/util/parser/ColumnMapper.java

    r3533 r3653  
    7575    @param nullIfException If TRUE, the mapper returns null for unparsable numeric
    7676      values, otherwise an excption is thrown
    77     @param parser The parser to use or null to use Float.valueOf()
     77    @param parser The parser to use or null to use Double.valueOf()
    7878    @since 2.4
    7979  */
     
    102102  public Integer getInt(Data data)
    103103  {
    104     return getFloat(getValue(data)).intValue();
     104    Double d = getDouble(getValue(data));
     105    return d == null ? null : d.intValue();
    105106  }
    106107  public Float getFloat(Data data)
    107108  {
    108     return getFloat(getValue(data));
     109    Double d = getDouble(getValue(data));
     110    return d == null ? null : d.floatValue();
    109111  }
    110112  // -------------------------------------------
     
    120122  // -------------------------------------------
    121123 
    122   private Float getFloat(String value)
     124  private Double getDouble(String value)
    123125  {
    124126    if (value == null) return null;
    125     Float f = null;
     127    Double d = null;
    126128    if (parser == null)
    127129    {
    128130      try
    129131      {
    130         f = Float.valueOf(value);
     132        d = Double.valueOf(value);
    131133      }
    132134      catch (RuntimeException rex)
     
    137139    else
    138140    {
    139       f = (Float)Type.FLOAT.parseString(value, parser, nullIfException);
     141      d = (Double)Type.DOUBLE.parseString(value, parser, nullIfException);
    140142    }
    141     return f;
     143    return d;
    142144  }
    143145 
  • branches/webservices/src/core/net/sf/basedb/util/parser/CompoundMapper.java

    r3533 r3653  
    117117        try
    118118        {
    119           intValue = Integer.parseInt(stringValue);
     119          intValue = Double.valueOf(stringValue).intValue();
    120120        }
    121121        catch (RuntimeException rex)
  • branches/webservices/src/core/net/sf/basedb/util/parser/ConstantMapper.java

    r3533 r3653  
    5959    Create a constant mapper using a specific number formatter as it's parser.
    6060    @param constant The constant expression
    61     @param parser The number format to use or null to use Float.valueOf()
     61    @param parser The number format to use or null to use Double.valueOf()
    6262    @since 2.2
    6363    @deprecated Use {@link ConstantMapper#ConstantMapper(String, NumberFormat, boolean)}
     
    7171    Create a constant mapper using a specific number formatter as it's parser.
    7272    @param constant The constant expression
    73     @param parser The number format to use or null to use Float.valueOf()
     73    @param parser The number format to use or null to use Double.valueOf()
    7474    @param nullIfException If TRUE, the mapper returns null for unparsable numeric
    7575      values, otherwise an excption is thrown
     
    151151      else
    152152      {
    153         asFloat = Float.valueOf(constant);
     153        asFloat = Double.valueOf(constant).floatValue();
    154154      }
    155155    }
  • branches/webservices/src/core/net/sf/basedb/util/parser/FlatFileParser.java

    <
    r3533 r3653  
    264264 
    265265  /**
     266    The number of data lines parsed in the current section so far.
     267    This value is reset at each new section.
     268  */
     269  private int parsedDataLines;
     270 
     271  /**
    266272    Map of header lines parsed by the {@link #parseHeaders()} method.
    267273    The map contains name -> value pairs
     
    648654            done = true;
    649655            lines.add(new Line(parsedLines, line, LineType.DATA));
    650             nextData = new Data(parsedLines, line, columns, emptyIsNull, nullIsNull);
     656            parsedDataLines = 1;
     657            nextData = new Data(parsedLines, parsedDataLines, line, columns, emptyIsNull, nullIsNull);
    651658          }
    652659        }
     
    851858    @param numberFormat The number format the mapper should use for
    852859      parsing numbers, or null to use Float.valueOf or Double.valueOf
    853     @param useNullIfException TRUE to return a null value instead of throwing
     860    @param nullIfException TRUE to return a null value instead of throwing
    854861      an exception when a value can't be parsed.
    855862    @return A mapper object
     
    969976        {
    970977          parsedLines++;
     978          parsedDataLines++;
    971979          parsedCharacters += line.length();
    972980         
     
    9971005            {
    9981006              done = true;
     1007              parsedDataLines = 0;
    9991008              nextSection = new Line(parsedLines, line, m.group(1), LineType.SECTION);
    10001009              lines.add(nextSection);
     
    10101019            {
    10111020              done = true;
    1012               nextData = new Data(parsedLines, line, columns, emptyIsNull, nullIsNull);
     1021              nextData = new Data(parsedLines, parsedDataLines, line, columns, emptyIsNull, nullIsNull);
    10131022            }
    10141023          }
     
    10561065  {
    10571066    return parsedLines;
     1067  }
     1068 
     1069  /**
     1070    Get the number of parsed data lines so far in the current section.
     1071    This value is reset for each new section.
     1072  */
     1073  public int getParsedDataLines()
     1074  {
     1075    return parsedDataLines;
    10581076  }
    10591077 
     
    11791197            done = true;
    11801198            nextSection = new Line(parsedLines, line, m.group(1), LineType.SECTION);