|
2.17.2: 2011-06-17 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Object net.sf.basedb.core.plugin.AbstractPlugin net.sf.basedb.plugins.AbstractFlatFileImporter net.sf.basedb.plugins.PlateMappingImporter
public class PlateMappingImporter
Importer for plate mappings. It has a fixed file format:
Source plates=1 Source rows=3 Source columns=3 Destination plates=1 Destination rows=3 Destination columns=3 Source plate Source row Source column Destination plate Destination row Destination column 0 0 0 0 0 0 0 0 1 0 1 0 0 0 2 0 2 0 0 1 0 0 0 1 0 1 1 0 1 1 0 1 2 0 2 1 0 2 0 0 0 2 0 2 1 0 1 2 0 2 2 0 2 2
Nested Class Summary |
---|
Nested classes/interfaces inherited from interface net.sf.basedb.core.plugin.Plugin |
---|
Plugin.MainType |
Field Summary | |
---|---|
private static About |
about
|
private RequestInformation |
configureJob
|
private DbControl |
dc
|
private static PluginParameter<String> |
descriptionParameter
|
private Mapper |
destColumnMapper
|
private Mapper |
destPlateMapper
|
private Mapper |
destRowMapper
|
private FlatFileParser |
ffp
|
private static Set<GuiContext> |
guiContexts
|
private static PluginParameter<String> |
nameParameter
|
private static Set<Permissions> |
permissions
|
private PlateMapping |
pm
|
private static StringParameterType |
requiredStringParameter
|
private Mapper |
sourceColumnMapper
|
private Mapper |
sourcePlateMapper
|
private Mapper |
sourceRowMapper
|
Fields inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
---|
annotationSection, configuration, COPY_ANNOTATIONS, job, OVERWRITE_ANNOTATIONS, sc |
Constructor Summary | |
---|---|
PlateMappingImporter()
Create a new importer. |
Method Summary | |
---|---|
protected void |
begin(FlatFileParser ffp)
Save reference to parser. |
protected void |
beginData()
Create a DbControl and a new PlateMapping . |
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 DbControl. |
private PlateGeometry |
findGeometry(DbControl dc,
int rows,
int columns)
|
About |
getAbout()
Get information about the plugin, such as name, version, authors, etc. |
private RequestInformation |
getConfigureJobParameters(GuiContext context)
|
Set<GuiContext> |
getGuiContexts()
Return a set containing the context:s [PLATEMAPPING, LIST]. |
protected FlatFileParser |
getInitializedFlatFileParser()
Create and initialise a flat file parser by setting all regular expressions and other options. |
Collection<Permissions> |
getPermissions()
Request create and write access to PlateMapping:s, create and use access to PlateGeometries and read access to File:s. |
RequestInformation |
getRequestInformation(GuiContext context,
String command)
This method will return the RequestInformation for a given command, i.e. |
protected String |
getSuccessMessage(int skippedLines)
Return Platemapping 'name' created. |
protected void |
handleData(FlatFileParser.Data data)
Add a mapping detail. |
String |
isInContext(GuiContext context,
Object item)
Always null. |
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.plugins.AbstractFlatFileImporter |
---|
addErrorHandler, checkColumnMapping, checkColumnMapping, continueWithNextFileAfterError, doImport, finish, getCharset, getCharset, getCharsetParameter, getDecimalSeparator, getDecimalSeparatorParameter, getErrorHandler, getErrorOption, getFileIterator, getMainType, getMapper, getNumberFormat, getNumBytes, getPrimaryLocationFilter, getProgress, getSignalHandler, getTotalFileSize, handleHeader, handleSection, isImportable, isImportable, log, log, log, log, run, setUpErrorHandling, start, wrapInputStream |
Methods inherited from class net.sf.basedb.core.plugin.AbstractPlugin |
---|
checkInterrupted, cloneParameterWithDefaultValue, closeLogFile, createLogFile, done, getCopyAnnotationsParmeter, getCurrentConfiguration, getCurrentJob, getJobOrConfigurationValue, getOverwriteAnnotationsParameters, init, log, log, storeValue, storeValue, storeValues, validateRequestParameters |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface net.sf.basedb.core.plugin.Plugin |
---|
done, getMainType, init, run |
Field Detail |
---|
private static final About about
private static final Set<GuiContext> guiContexts
private static final Set<Permissions> permissions
private static final StringParameterType requiredStringParameter
private RequestInformation configureJob
private static final PluginParameter<String> nameParameter
private static final PluginParameter<String> descriptionParameter
private DbControl dc
private PlateMapping pm
private Mapper sourcePlateMapper
private Mapper sourceRowMapper
private Mapper sourceColumnMapper
private Mapper destPlateMapper
private Mapper destRowMapper
private Mapper destColumnMapper
private FlatFileParser ffp
Constructor Detail |
---|
public PlateMappingImporter()
Method Detail |
---|
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)
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 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
throughpublic RequestInformation getRequestInformation(GuiContext context, String command) throws BaseException
InteractivePlugin
RequestInformation
for a given command, i.e.
the list of parameters and some nice help text.
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 errorprotected void begin(FlatFileParser ffp) throws BaseException
begin
in class AbstractFlatFileImporter
BaseException
AbstractFlatFileImporter.end(boolean)
protected void beginData()
DbControl
and a new PlateMapping
.
Initialise column Mapper
:s.
beginData
in class AbstractFlatFileImporter
protected void handleData(FlatFileParser.Data data) throws BaseException
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)
Platemapping 'name' created.
.
getSuccessMessage
in class AbstractFlatFileImporter
skippedLines
- The number of data lines that were skipped due to errorsprotected FlatFileParser getInitializedFlatFileParser() throws BaseException
AbstractFlatFileImporter
AbstractPlugin.job
or AbstractPlugin.configuration
settings. If a subclass doesn't store the
parameters there it must override this method and initialise the parser. Note that
this method is called once for each file returned by the
AbstractFlatFileImporter.getFileIterator()
and that a new parser is needed for each file.
getInitializedFlatFileParser
in class AbstractFlatFileImporter
BaseException
private RequestInformation getConfigureJobParameters(GuiContext context)
private PlateGeometry findGeometry(DbControl dc, int rows, int columns)
|
2.17.2: 2011-06-17 | ||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |