Package net.sf.basedb.core

Class PluginConfiguration

java.lang.Object
net.sf.basedb.core.BasicItem
net.sf.basedb.core.OwnedItem
net.sf.basedb.core.SharedItem
net.sf.basedb.core.CommonItem
net.sf.basedb.core.AnnotatedItem
net.sf.basedb.core.PluginConfiguration
All Implemented Interfaces:
AccessControlled, Annotatable, AnnotatableProxy, Controlled, Identifiable, Nameable, Ownable, Registered, Removable, Shareable, Transactional
public class PluginConfiguration
extends AnnotatedItem
implements Transactional, AnnotatableProxy, Registered
This class is used to configure a plugin. A plugin can have many configurations.
Version:
2.0
Author:
Nicklas, Samuel

  • Field Details

  • Constructor Details

  • Method Details

    • getNew

      public static PluginConfiguration getNew​(DbControl dc, PluginDefinition pd) throws PermissionDeniedException, BaseException
      Create a new PluginConfiguration item.
      Parameters:
      dc - The DbControl which will be used for permission checking and database access.
      pd - PluginDefinition to create a configuration for.
      Returns:
      The new PluginConfiguration item
      Throws:
      InvalidDataException - If the plugin definition is null
      PermissionDeniedException - If the logged in user doesn't have use permission for the plugin definition
      BaseException - If there is an error

    • getById

      public static PluginConfiguration getById​(DbControl dc, int id) throws ItemNotFoundException, PermissionDeniedException, BaseException
      Get a PluginConfiguration item when you know the ID.
      Parameters:
      dc - The DbControl which will be used for permission checking and database access.
      id - The ID of the item to load
      Returns:
      The PluginConfiguration item
      Throws:
      ItemNotFoundException - If an item with the specified ID is not found
      PermissionDeniedException - If the logged in user doesn't have READ permission for the item
      BaseException - If there is another error

    • getQuery

      public static ItemQuery<PluginConfiguration> getQuery()
      Get a query configured to retrieve plugin configurations.
      Returns:
      An ItemQuery object

    • getQuery

      public static ItemQuery<PluginConfiguration> getQuery​(GuiContext gc, String interfaceName)
      Get a query that returns all plugins configurations related to a specified GUI context and implementing a certain interface. Ie. The PluginDefinition.isInContext(GuiContext) returns true for the specified item, and PluginDefinition.supports(PluginType) returns true for the specified interface.
      Parameters:
      gc - The item the plugin should be related to, or null if this parameter is irrelevant
      interfaceName - The complete name of the interface that the plugin must implement, or null if this parameter is irrelevant

    • loadXmlFile2

      public static List<Element> loadXmlFile2​(InputStream in, String fileName) throws IOException
      Load a configurations xml file from the given stream.
      Parameters:
      in - The input stream to read from
      fileName - The name of the originating file (optional)
      Returns:
      A list with all <configuration> elements in the file
      Throws:
      IOException
      Since:
      3.4

    • getData

      PluginConfigurationData getData()
      Description copied from class: BasicItem
      Get the BasicData object that holds all data for this item.
      Overrides:
      getData in class AnnotatedItem

    • getType

      public Item getType()
      Description copied from interface: Identifiable
      Get the type of item represented by the object. The returned value is one of the values defined in the Item enumeration.
      Specified by:
      getType in interface Identifiable
      Returns:
      A value indicating the type of item

    • getEntryDate

      public Date getEntryDate()
      Description copied from interface: Registered
      Get the date that the item was registered in the database.
      Specified by:
      getEntryDate in interface Registered
      Returns:
      A date or null if this is not known

    • setEntryDate

      public void setEntryDate​(Date entryDate)
      Description copied from interface: Registered
      Set the date the entry was registered in the database. Implementations should only allow this property to be set before the item is first stored in the database. The intention of this method is to facilitate export/import of data between server.
      Specified by:
      setEntryDate in interface Registered
      Parameters:
      entryDate - A date or null to use today's date

    • isUsed

      public boolean isUsed() throws BaseException
      Check if:
      • A Job is using this plugin configuration
      Overrides:
      isUsed in class BasicItem
      Returns:
      TRUE if this item is used, FALSE otherwise
      Throws:
      BaseException - If not able to tell if item is used or not.
      See Also:
      BasicItem.getUsingItems()

    • getUsingItems

      public Set<ItemProxy> getUsingItems()
      Get all:
      • Job:s using this configuration
      Overrides:
      getUsingItems in class BasicItem
      Returns:
      A set containing proxies for the items, or an empty set if no items are using this item
      Since:
      2.2
      See Also:
      BasicItem.addUsingItems(Set, Item, org.hibernate.query.Query)

    • onAfterCommit

      void onAfterCommit​(Transactional.Action action)
      Reset parameter version so that adding new parameters will increase the version the next time.
      Overrides:
      onAfterCommit in class BasicItem
      See Also:
      Transactional, Developer documentation: Transactions, Developer documentation: Coding rules and guidelines for item classes

    • getAnnotatableParents

      public Set<Annotatable> getAnnotatableParents()
      Description copied from interface: Annotatable
      Get all parents objects which are annotatable and the logged in user has read permission to. If the item doesn't have any annotatable parents, it may return null or an empty set. The method should only return the immediate parent(s), not parents to parents, etc. As of BASE 3.1 this method may also return child items if the child item is a Subtypable item that has a subtype with the ItemSubtype.getPushAnnotations() flag set.
      Specified by:
      getAnnotatableParents in interface Annotatable
      Returns:
      Always null
      Since:
      2.5

    • getAnnotationTypes

      public ItemQuery<AnnotationType> getAnnotationTypes()
      Get the annotation types that can be used by this configuration. This method requires that the plug-in implements the AnnotationSetterPlugin interface.
      Specified by:
      getAnnotationTypes in interface AnnotatableProxy
      Returns:
      A query or null if this plug-in doesn't use annotations
      Since:
      2.5

    • getAnnotationMessage

      public String getAnnotationMessage()
      Get a message explaining what the proxy does with the annotations.
      Specified by:
      getAnnotationMessage in interface AnnotatableProxy
      Returns:
      A message or null
      Since:
      2.5

    • getPluginDefinition

      public PluginDefinition getPluginDefinition() throws PermissionDeniedException, BaseException
      Get the plugin definition for this configuration.
      Returns:
      PluginDefinition object.
      Throws:
      PermissionDeniedException - This exception is thrown if the logged in user doesn't have READ permission to the items.
      BaseException - If anything else fails.

    • setPluginDefinition

      private void setPluginDefinition​(PluginDefinition pd) throws PermissionDeniedException, InvalidUseOfNullException
      The definition cannot be changed. Used internally only.
      Throws:
      PermissionDeniedException
      InvalidUseOfNullException

    • isDisabled

      public boolean isDisabled()
      Checks if this plugin configuration is disabled or not. A disabled configuration can't be used.
      Since:
      3.19.6

    • setDisabled

      public void setDisabled​(boolean disabled)
      Disabled or enable this plugin configuration.
      Since:
      3.19.6

    • getParameterVersion

      public int getParameterVersion()
      Get the latest version number of the parameters.

    • getNewParameterVersion

      private int getNewParameterVersion()
      Increase the version number once per transaction.

    • getParameterNames

      public Set<String> getParameterNames()
      Get the names of all configuration values in the latest version.
      Returns:
      A Set containing the names of the configuration values or an empty set if no values has been defined
      See Also:
      getParameterNames(int)

    • getParameterNames

      public Set<String> getParameterNames​(int version)
      Get the names of all configuration values in a specific version.
      Parameters:
      version - The version to get the configuration parameters for
      Returns:
      A Set containing the names of the configuration values or an empty set if no values has been defined
      See Also:
      getParameterNames()

    • getParameterValues

      public List<?> getParameterValues​(String name) throws PermissionDeniedException, BaseException
      Get the values of a configuration parameter in the latest version.
      Parameters:
      name - The name of the parameter
      Returns:
      The values, or null if no value has been set
      Throws:
      PermissionDeniedException - If the logged in user doesn't have read permission to all values
      BaseException - If there is another error
      See Also:
      getParameterValues(String, int)

    • getParameterValues

      public List<?> getParameterValues​(String name, int version) throws PermissionDeniedException, BaseException
      Get the values of a configuration parameter in a specific version.
      Parameters:
      name - The name of the parameter
      version - The version of the parameter
      Returns:
      The values, or null if no value has been set
      Throws:
      PermissionDeniedException - If the logged in user doesn't have read permission to all values
      BaseException - If there is another error
      See Also:
      getParameterValues(String)

    • getParameterInfo

      public ParameterInfo getParameterInfo​(String name) throws PermissionDeniedException, BaseException
      Get extra information about a parameter in the latest version. The information includes the label, description and values of the parameter.
      Parameters:
      name - The name of the parameter
      Returns:
      A ParameterInfo object or null if no parameter with the specified name exists
      Throws:
      PermissionDeniedException - If the parameter contain values that the logged in user doesn't have read permission for
      BaseException - If there is another error
      See Also:
      getParameterInfo(String, int)

    • getParameterInfo

      public ParameterInfo getParameterInfo​(String name, int version) throws PermissionDeniedException, BaseException
      Get extra information about a parameter in a specific version. The information includes the label, description and values of the parameter.
      Parameters:
      name - The name of the parameter
      version - The version of the parameter
      Returns:
      A ParameterInfo object or null if no parameter with the specified name exists
      Throws:
      PermissionDeniedException - If the parameter contain values that the logged in user doesn't have read permission for
      BaseException - If there is another error
      See Also:
      getParameterInfo(String)

    • getParameterValues

      public ParameterValues getParameterValues​(int version)
      Get the configuration parameters as a ParameterValues object.
      Parameters:
      version - The version of the parameters
      Returns:
      A ParameterValues object
      Since:
      2.5
      See Also:
      getParameterVersion()

    • setParameterValues

      public void setParameterValues​(String name, ParameterType<?> parameterType, List<?> values) throws InvalidDataException, PermissionDeniedException, BaseException
      Set a configuration parameter. The parameter version number is increased by one when the values are committed to the database.
      Parameters:
      name - The name of the configuration parameter
      parameterType - The type of the parameter
      values - A list containing the new values, null or empty to remove the configuration values
      Throws:
      PermissionDeniedException - If the logged in user doesn't have write permission
      InvalidDataException - If name is null or the new value doesn't validate against the parameter type
      BaseException - If there is another error

    • setParameterValues

      public void setParameterValues​(String name, String label, String description, ParameterType<?> parameterType, List<?> values) throws InvalidDataException, PermissionDeniedException, BaseException
      Set a configuration parameter. The parameter version number is increased by one when the values are committed to the database.
      Parameters:
      name - The name of the configuration parameter
      label - The label of the parameter (optional)
      description - A description of the parameter (optional)
      parameterType - The type of the parameter
      values - A list containing the new values, null or empty to remove the configuration values
      Throws:
      PermissionDeniedException - If the logged in user doesn't have write permission
      InvalidDataException - If name is null or the new value doesn't validate against the parameter type
      BaseException - If there is another error

    • setParameterValuesInternal

      void setParameterValuesInternal​(String name, String label, String description, ParameterType<?> parameterType, List<?> values, boolean validate) throws InvalidDataException, PermissionDeniedException, BaseException
      Set the values of a configuration parameter.
      Parameters:
      name - The name of the configuration parameter
      label - The label of the parameter (optional)
      description - A description of the parameter (optional)
      parameterType - The type of the parameter
      values - A list containing the new values, null or empty to remove the configuration values
      validate - If validation by ParameterType.validate(String, List) is needed or not
      Throws:
      PermissionDeniedException - If the logged in user doesn't have write permission
      InvalidDataException - If name is null or the new value doesn't validate against the parameter type
      BaseException - If there is another error

    • copyParametersFrom

      public void copyParametersFrom​(PluginConfiguration copyFrom) throws InvalidDataException, PermissionDeniedException, BaseException
      Copy all parameter values from another plugin configuration. This method increases the parameter version number and saves the copied parameters in that version.
      Parameters:
      copyFrom - The configuration to copy parameters from
      Throws:
      InvalidDataException - If the copyFrom parameter is null
      PermissionDeniedException - If the logged in user doesn't have write permission for this configuration
      BaseException - If there is another error

    • configure

      public PluginConfigurationRequest configure() throws PermissionDeniedException, BaseException
      Start the configuration sequence for a plugin. See PluginRequest for more information. The parameters sent to the plugin are those from the latest version.
      Returns:
      A PluginRequest object
      Throws:
      PermissionDeniedException - If the logged in user doesn't have write permission
      BaseException - If there is another error

    • newJob

      public Job newJob​(Experiment experiment) throws PermissionDeniedException, BaseException
      Create a new Job for this plugin configuration.
      Parameters:
      experiment - The experiment the job is part of, or null if the job is not part of an experiment
      Returns:
      The new Job item
      Throws:
      PermissionDeniedException - If the logged in user doesn't have use permission for this plugin definition
      BaseException
      Since:
      2.7

    • getJobs

      public ItemQuery<Job> getJobs()
      Get a query that returns the jobs using this plugin configuration.
      Returns:
      An ItemQuery object

    • getParameterValuesImpl

      ParameterValuesImpl getParameterValuesImpl​(int version) throws BaseException
      Get a write-protected ParameterValuesImpl object so a job can read the paremeters.
      Throws:
      BaseException

    • setParameterValues2

      public void setParameterValues2​(List<Element> parameters) throws ClassNotFoundException
      Sets parameters for a PluginConfiguration from the elements in a xml configurations file.
      Parameters:
      parameters - A list of the parameters that shall be set to the configuration
      Throws:
      ClassNotFoundException - If there is an error while trying to find the type of the parameters.
      Since:
      3.4

    • getValueList2

      private <T> List<T> getValueList2​(Element parameter, Class<T> classType)
      Gets the list of values for a parameter from the XML-file. Returns a list with parameter values.

    • getParameterType

      private <T> ParameterType<T> getParameterType​(Class<T> parameterClass, List<?> values)
      Gets the ParameterType to use with a class. Returns null if this importer doesn't support the class.