Class AbstractAnalysisPlugin

    • Constructor Detail

      • AbstractAnalysisPlugin

        protected AbstractAnalysisPlugin()
        Create a new AbstractAnalysisPlugin.
    • Method Detail

      • isInContext

        public String isInContext​(GuiContext context,
                                  Object item)
        Check that the item is a bioassayset/derived bioassay and that the logged in user has permission to use the current item.
        Parameters:
        context - Current guicontext
        item - The item to check.
        Returns:
        null if the item is a valid item, an error message otherwise
        Throws:
        PermissionDeniedException - If the logged in user dosen't have permission to use the Experiment
      • getSourceBioAssaySetParameter

        protected PluginParameter<BioAssaySet> getSourceBioAssaySetParameter​(String label,
                                                                             String description)
        Get a plugin parameter that asks for a bioassay set to use as data source for the plugin. Calling this method multiple times return the same plugin parameter object. The label and description for the first call is always used.
        Parameters:
        label - The parameter label, or null to use the default (Source bioasay set)
        description - The parameter description, or null to use the default (The bioassay set that is used as the data source for this job.)
      • getSourceDerivedBioAssayParameter

        protected PluginParameter<DerivedBioAssay> getSourceDerivedBioAssayParameter​(String label,
                                                                                     String description)
        Get a plugin parameter that asks for a derived bioassay to use as data source for the plugin. Calling this method multiple times return the same plugin parameter object. The label and description for the first call is always used.
        Parameters:
        label - The parameter label, or null to use the default (Source bioassay)
        description - The parameter description, or null to use the default (The derived bioassay that is used as the data source for this job.)
      • getSourceBioAssaysParameter

        protected PluginParameter<BioAssay> getSourceBioAssaysParameter​(String label,
                                                                        String description)
        Gets a plugin parameter that asks for a subset of bioassays to use as data source for the plugin.
        Parameters:
        label - The parameter's label. Uses a default value if null.
        description - Description of the parameter. Uses a default value if null.
        Returns:
        A plugin parameter
        Since:
        2.4
      • getChildNameParameter

        protected PluginParameter<String> getChildNameParameter​(String label,
                                                                String description,
                                                                String defaultValue)
        Create a plugin parameter that asks for the name of the child bioassay set.
        Parameters:
        label - The label to use for the parameter or null to use the default label (Child name)
        description - The description to use for the parameter or null to use the default description (The name of the child bioassay set)
        defaultValue - The default value for the child name or null to use the default value (New bioassay set)
        Returns:
        A plugin parameter
      • getChildDescriptionParameter

        protected PluginParameter<String> getChildDescriptionParameter​(String label,
                                                                       String description,
                                                                       String defaultValue)
        Create a plugin parameter that asks for the description of the child bioassay set.
        Parameters:
        label - The label to use for the parameter or null to use the default label (Child description)
        description - The description to use for the parameter or null to use the default description (An optional description of the child bioassay set)
        defaultValue - The default value for the child name or null to not use any default value
        Returns:
        A plugin parameter
      • getTransformationNameParameter

        protected PluginParameter<String> getTransformationNameParameter​(String label,
                                                                         String description,
                                                                         String defaultValue)
        Create a plugin parameter that asks for the name of the transformation.
        Parameters:
        label - The label to use for the parameter or null to use the default label (Transformation name)
        description - The description to use for the parameter or null to use the default description (The name of the transformation)
        defaultValue - The default value for the transformation name or null to not use any default
        Returns:
        A plugin parameter
      • getCurrentExperiment

        protected Experiment getCurrentExperiment​(DbControl dc)
        Get the current experiment from information in the current context: SessionControl.getCurrentContext(Item.EXPERIMENT). Note that this information is normally only available during the configuration phase of a plugin, not during the execution phase.
        Parameters:
        dc - The DbControl to use for database access
        Returns:
        The current experiment or null
      • getCurrentBioAssaySet

        protected BioAssaySet getCurrentBioAssaySet​(DbControl dc)
        Get the current source bioassay set. We first check the job's parameter values with the getSourceBioAssaySet(DbControl) method. If this returns null we check the information in the current context: SessionControl.getCurrentContext(Item.BIOASSAYSET). Note that this information is normally only available during the configuration phase of a plugin, not during the execution phase.
        Parameters:
        dc - The DbControl to use for database access
        Returns:
        The current bioassay set or null
        See Also:
        getSourceBioAssaySet(DbControl)
      • getSourceBioAssaySet

        protected BioAssaySet getSourceBioAssaySet​(DbControl dc)
        Get the bioassay set that is used as the source for the plugin. The source bioassay set is only available in the execution phase if the plugin has saved it as a job parameter during the configuration of a job.
        Returns:
        The source bioassay set or null
        See Also:
        getSourceBioAssaySetParameter(String, String)
      • getSourceBioAssays

        protected List<BioAssay> getSourceBioAssays​(DbControl dc)
        Gets a list of bioassays that were selected from the current bioassay set, to use for the analysis.
        Parameters:
        dc - The DbControl to access the database with
        Returns:
        A list with bioassays or null.
        Since:
        2.4
      • getCurrentDerivedBioAssay

        protected DerivedBioAssay getCurrentDerivedBioAssay​(DbControl dc)
        Get the current source derived bioassay. We first check the job's parameter values with the getSourceDerivedBioAssay(DbControl) method. If this returns null we check the information in the current context: SessionControl.getCurrentContext(Item.DERIVEDBIOASSAY). Note that this information is normally only available during the configuration phase of a plugin, not during the execution phase.
        Parameters:
        dc - The DbControl to use for database access
        Returns:
        The current derived bioassay or null
        Since:
        3.0
        See Also:
        getSourceBioAssaySet(DbControl)
      • getSourceDerivedBioAssay

        protected DerivedBioAssay getSourceDerivedBioAssay​(DbControl dc)
        Get the derived bioassay that is used as the source for the plugin. The source bioassay is only available in the execution phase if the plugin has saved it as a job parameter during the configuration of a job.
        Returns:
        The source derived bioassay or null
        Since:
        3.0
        See Also:
        getSourceDerivedBioAssayParameter(String, String)
      • getTransformationName

        protected String getTransformationName​(DbControl dc)
        Generate a name for the transformation based on the plugin and it's configuration. The name is created by taking the name of the plugin from the About.getName() method and combine it with the configuration used. If no configuration is used only the plugin name is used.
        Parameters:
        dc - The DbControl to use for database access
        Returns:
        A name for the transformation
      • restrictSource

        protected DynamicSpotQuery restrictSource​(DynamicSpotQuery query,
                                                  List<BioAssay> bioAssays)
        Restricts a query to only include values from listed bioassays
        Parameters:
        query - The query to set restriction on
        bioAssays - A list with bioassays the restriction should include
        Returns:
        A DynamicSpotQuery object. The query parameter is restricted if bioAssays holds item(s), otherwise it will it will be the same
        Since:
        2.4