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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.plugins.AbstractFlatFileImporter net.sf.basedb.plugins.PlateFlatFileImporter
public class PlateFlatFileImporter
Nested Class Summary |
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Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin |
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Plugin.MainType |
Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc |
Constructor Summary | |
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PlateFlatFileImporter()
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Method Summary | |
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protected void |
begin(FlatFileParser ffp)
Create a DbControl and a RawDataBatcher . |
protected void |
beginData()
Initialise column Mapper :s. |
void |
configure(GuiContext context,
Request request,
Response response)
Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN
and Request.COMMAND_CONFIGURE_JOB . |
protected void |
end(boolean success)
Close and commit/rollback and DbControl. |
About |
getAbout()
Get information about the plugin, such as name, version, authors, etc. |
private List<PluginParameter<String>> |
getAllColumnMappings()
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private RequestInformation |
getConfigureJobParameters(GuiContext context)
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private RequestInformation |
getConfigurePluginParameters(GuiContext context)
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Set<GuiContext> |
getGuiContexts()
Get a set containing all items that the plugin handles. |
Collection<Permissions> |
getPermissions()
Request create access to Plate:s, use access to PlateType:s and read access to Reporter:s, PlateGeometry:s and File:s. |
RequestInformation |
getRequestInformation(GuiContext context,
String command)
The Request.COMMAND_CONFIGURE_PLUGIN command will ask for
parser regular expressions and column mappings. |
protected String |
getSuccessMessage(int skippedLines)
Return x plates inserted . |
protected void |
handleData(FlatFileParser.Data data)
Called by the parser for every line in the file that is a data line. |
String |
isInContext(GuiContext context,
Object item)
Always null, since plugin doesn't operate on individual items. |
boolean |
requiresConfiguration()
Return TRUE, since the implementation requires it for finding the regular expressions used by the FlatFileParser . |
boolean |
supportsConfigurations()
Returns TRUE, since that is how the plugins used to work before this method was introduced. |
Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
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checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.plugin.Plugin |
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done, getMainType, init, run |
Field Detail |
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private static final About about
private static final Set<GuiContext> guiContexts
private static final Set<Permissions> permissions
private static final PluginParameter<String> columnColumnMapping
private static final PluginParameter<String> rowColumnMapping
private static final PluginParameter<String> reporterColumnMapping
private static final PluginParameter<String> nameColumnMapping
private static final PluginParameter<String> barcodeColumnMapping
private PluginParameter<String> plateNamePrefixParameter
private PluginParameter<String> reporterPrefixParameter
private PluginParameter<Integer> namePaddingParameter
protected static final PluginParameter<String> missingReporterErrorParameter
private ItemParameterType<PlateType> plateTypeType
private PluginParameter<PlateType> plateTypeParameter
private List<PluginParameter<String>> allColumnMappings
private RequestInformation configurePlugin
private RequestInformation configureJob
private DbControl dc
private FlatFileParser ffp
private int numPlates
private int numWells
private PlateType plateType
private String plateNamePrefix
private Integer plateNamePadding
private String reporterPrefix
private Mapper reporterMapper
private Mapper nameMapper
private Mapper barcodeMapper
private Mapper rowMapper
private Mapper columnMapper
private ReporterBatcher reporterBatcher
private boolean errorIfNotFound
private HashMap<String,Plate> plates
Constructor Detail |
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public PlateFlatFileImporter()
Method Detail |
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public About getAbout()
Plugin
getAbout
in interface Plugin
About
objectpublic boolean supportsConfigurations()
AbstractPlugin
supportsConfigurations
in interface Plugin
supportsConfigurations
in class AbstractPlugin
public boolean requiresConfiguration()
AbstractFlatFileImporter
FlatFileParser
. If this
method is overridden and returns FALSE, the subclass must also override
the AbstractFlatFileImporter.getInitializedFlatFileParser()
method and provide a
parser with all regular expressions and other options set.
requiresConfiguration
in interface Plugin
requiresConfiguration
in class AbstractFlatFileImporter
public Collection<Permissions> getPermissions()
getPermissions
in interface Plugin
getPermissions
in class AbstractPlugin
public Set<GuiContext> getGuiContexts()
InteractivePlugin
Item.REPORTER
.
This information is used by client applications to put the plugin
in the proper place in the user interface.
getGuiContexts
in interface InteractivePlugin
Set
containing Item
:s, or null
if the plugin is not concerned about itemspublic String isInContext(GuiContext context, Object item)
isInContext
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
item
- The currently active item, it's type should match the
GuiContext.getItem()
type, or null if the context is a list
context
Null
if the plugin can use that item, or
a warning-level message explaining why the plugin can't be usedpublic RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
Request.COMMAND_CONFIGURE_PLUGIN
command will ask for
parser regular expressions and column mappings.
The Request.COMMAND_CONFIGURE_JOB
command will ask for
a file and what PlateType
the plates in the file has.
getRequestInformation
in interface InteractivePlugin
command
- context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
RequestInformation
for the command
BaseException
- if there is an errorpublic void configure(GuiContext context, Request request, Response response)
Request.COMMAND_CONFIGURE_PLUGIN
and Request.COMMAND_CONFIGURE_JOB
.
configure
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
request
- Request object with the command and parametersresponse
- Response object in for the plugin to response
throughprotected void begin(FlatFileParser ffp) throws BaseException
DbControl
and a RawDataBatcher
.
Load the RawBioAssay
that has been specified.
begin
in class AbstractFlatFileImporter
BaseException
AbstractFlatFileImporter.end(boolean)
protected void beginData()
Mapper
:s.
beginData
in class AbstractFlatFileImporter
protected void end(boolean success) throws BaseException
end
in class AbstractFlatFileImporter
success
- TRUE if the file was parsed successfully, FALSE otherwise
BaseException
AbstractFlatFileImporter.begin(FlatFileParser)
protected void handleData(FlatFileParser.Data data) throws BaseException
AbstractFlatFileImporter
handleData
in class AbstractFlatFileImporter
BaseException
protected String getSuccessMessage(int skippedLines)
x plates inserted
.
getSuccessMessage
in class AbstractFlatFileImporter
skippedLines
- The number of data lines that were skipped due to errorsprivate RequestInformation getConfigurePluginParameters(GuiContext context)
private RequestInformation getConfigureJobParameters(GuiContext context)
private List<PluginParameter<String>> getAllColumnMappings()
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2.17.2: 2011-06-17 | ||||||||
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