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java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.plugins.AbstractFlatFileImporter net.sf.basedb.plugins.ReporterMapFlatFileImporter
public class ReporterMapFlatFileImporter
A plugin that imports features to an ArrayDesign from a flat file. The ArrayDesign will not have any connections to plates.
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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ReporterMapFlatFileImporter()
Create a new importer. |
Method Summary | |
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protected void |
begin(FlatFileParser ffp)
Create a DbControl and a FeatureBatcher . |
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 the FeatureBatcher 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()
Return a set containing the element [ARRAYDESIGN, ITEM]. |
Collection<Permissions> |
getPermissions()
Request write access to ArrayDesign:s, read access to Reporter:s, DataFileType:s, Platform: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 features inserted; y blocks 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)
Returns null if the item is a ArrayDesign that doesn't already have
any features and isn't an affy design. |
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 StringParameterType requiredColumnMapping
private static final StringParameterType optionalColumnMapping
private static final PluginParameter<String> featureIdentificationParameter
private static final PluginParameter<String> reporterIdColumnMapping
private static final PluginParameter<String> featureIdColumnMapping
private static final PluginParameter<String> positionColumnMapping
private static final PluginParameter<String> blockColumnMapping
private static final PluginParameter<String> metaGridXColumnMapping
private static final PluginParameter<String> metaGridYColumnMapping
private static final PluginParameter<String> columnColumnMapping
private static final PluginParameter<String> rowColumnMapping
protected static final PluginParameter<String> missingReporterErrorParameter
protected static final PluginParameter<String> duplicateFeatureErrorParameter
private RequestInformation configurePlugin
private RequestInformation configureJob
private DbControl dc
private FeatureBatcher batcher
private ReporterBatcher reporterBatcher
private FileSetMember reporterMapMember
private ArrayDesign arrayDesign
private Map<BlockInfo,ArrayDesignBlock> blocks
private FlatFileParser ffp
private ItemParameterType<ArrayDesign> arrayDesignType
private PluginParameter<ArrayDesign> arrayDesignParameter
private List<PluginParameter<String>> allColumnMappings
private boolean errorIfNotFound
private Mapper reporterMapper
private Mapper featureIdMapper
private Mapper positionMapper
private Mapper blockMapper
private Mapper columnMapper
private Mapper rowMapper
private Mapper metaGridXMapper
private Mapper metaGridYMapper
private int numFeatures
private int numBlocks
Constructor Detail |
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public ReporterMapFlatFileImporter()
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()
getGuiContexts
in interface InteractivePlugin
Set
containing Item
:s, or null
if the plugin is not concerned about itemspublic String isInContext(GuiContext context, Object item)
ArrayDesign
that doesn't already have
any features and isn't an affy design.
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 used
PermissionDeniedException
- If the array design already has features
or if the logged in user doesn't have write permissionpublic 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 the array design that features should be added to.
getRequestInformation
in interface InteractivePlugin
context
- The current context of the client application,
it is one of the values found in set returned by InteractivePlugin.getGuiContexts()
command
- The command
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 FeatureBatcher
.
Check that the ArrayDesign
doesn't already have features.
begin
in class AbstractFlatFileImporter
BaseException
AbstractFlatFileImporter.end(boolean)
protected void beginData()
Mapper
:s.
beginData
in class AbstractFlatFileImporter
protected void handleData(FlatFileParser.Data data) throws BaseException
AbstractFlatFileImporter
handleData
in class AbstractFlatFileImporter
BaseException
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 String getSuccessMessage(int skippedLines)
x features inserted; y blocks inserted
.
getSuccessMessage
in class AbstractFlatFileImporter
skippedLines
- The number of data lines that were skipped due to errorsprivate List<PluginParameter<String>> getAllColumnMappings()
private RequestInformation getConfigureJobParameters(GuiContext context)
private RequestInformation getConfigurePluginParameters(GuiContext context)
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2.17.2: 2011-06-17 | ||||||||
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