SPECCHIOClient (SPECCHIO 3.3.0 API)

All Known Implementing Classes:

SPECCHIOClientCache, SPECCHIOWebClient
```
public interface SPECCHIOClient
```
This interfaces defines all of the methods to be implemented by a SPECCHIO client.

Method Summary

All Methods Instance Methods Abstract Methods
Modifier and Type	Method and Description
`void`	`calculateSunAngle(java.util.ArrayList<java.lang.Integer> spectrumIds, SPECCHIOClient client)` Get metaparameters for spectrum ids and EAV attribute
`void`	`clearMetaparameterRedundancyList()` Clears the known metaparameter list held by the server for this user
`void`	`close()` Close this client
`void`	`connect()` Connect to the server.
`int`	`copyHierarchy(int hierarchy_id, int target_hierarchy_id, java.lang.String new_name)` Copy a hierarchy to a specified hierarchy with a new name.
`java.util.ArrayList<java.lang.Integer>`	`copySpectra(java.util.ArrayList<java.lang.Integer> spectrum_id, int target_hierarchy_id, int current_hierarchy_id)` Copy a spectrum to a specified hierarchy.
`int`	`copySpectrum(int spectrum_id, int target_hierarchy_id)` Copy a spectrum to a specified hierarchy.
`void`	`createFilterCollection(java.util.ArrayList<java.lang.Integer> specturmIds, java.util.ArrayList<java.lang.Integer> attributeIds)`
`void`	`createInstrument(java.lang.String name)` Create a new instrument.
`void`	`createReference(java.lang.String name)` Create a new reference.
`User`	`createUserAccount(User user)` Create a user account.
`User`	`createUserAccountOnCurrentServer(User user)` Create a user account on this specchio server.
`void`	`dbUpgrade(double version, java.io.FileInputStream fis)` Database upgrade
`void`	`deleteCalibration(int calibration_id)` Delete calibration data from the database
`void`	`deleteInstrument(int instrument_id)` Delete an instrument from the database.
`void`	`deleteInstrumentPicture(int picture_id)` Delete a picture of an instrument from the database.
`void`	`deleteReference(int reference_id)` Delete a reference from the database.
`void`	`deleteReferencePicture(int picture_id)` Delete a picture of a reference from the database.
`int`	`deleteTargetReferenceLinks(int eav_id)` Delete target-reference links from the database.
`void`	`disconnect()` Disconnect from the server.
`java.util.ArrayList<java.lang.Integer>`	`filterSpectrumIdsByHavingAttribute(java.util.ArrayList<java.lang.Integer> spectrum_ids, java.lang.String attribute_name)` Get the spectrum identifiers that do have a reference to the specified attribute.
`java.util.ArrayList<java.lang.Integer>`	`filterSpectrumIdsByHavingAttributeValue(java.util.ArrayList<java.lang.Integer> spectrum_ids, java.lang.String attribute_name, java.lang.Object value)` Get the spectrum identifiers that do reference to the specified attribute of a specified value.
`java.util.ArrayList<java.lang.Integer>`	`filterSpectrumIdsByNotHavingAttribute(java.util.ArrayList<java.lang.Integer> spectrum_ids, java.lang.String attribute_name)` Get the spectrum identifiers that do not have a reference to the specified attribute.
`java.util.ArrayList<java.lang.Integer>`	`findMatchingSpectra(java.util.ArrayList<java.lang.Integer> spectrumIds, java.util.ArrayList<QueryAttribute> queryAttributes)`
`AdjacencyMatrix`	`getAdjacencyMatrix(int uncertainty_set_id)` Get the adjacency matrix for a given uncertainty set
`attribute[]`	`getAttributes()` Get the attributes object containing information on all attributes, units and categories.
`attribute[]`	`getAttributesForCategory(java.lang.String category)` Get the attributes for a metadata category.
`java.util.Hashtable<java.lang.Integer,attribute>`	`getAttributesIdHash()` Get the attributes hashtable
`java.util.Hashtable<java.lang.String,attribute>`	`getAttributesNameHash()` Get the attributes hashtable
`Units`	`getAttributeUnits(attribute attr)` Get the units for an attribute.
`Instrument`	`getCalibratedInstrument(int calibration_id)` Get a calibrated instrument.
`java.util.ArrayList<java.lang.Integer>`	`getCalibrationIds(java.util.ArrayList<java.lang.Integer> spectrum_ids)` Get calibration ids for a list of spectra.
`CalibrationMetadata[]`	`getCalibrationMetadataByCalibrationNumber(int instrument_id, int calibration_number)` Get an array of CalibrationMetadata based on an instrument id and a calibration number (typically an ASD instrument).
`Campaign`	`getCampaign(int campaign_id)` Get a campaign descriptor.
`java.io.InputStream`	`getCampaignExportInputStream(Campaign c)` Export a campaign.
`campaign_node`	`getCampaignNode(int campaign_id, java.lang.String order_by, boolean restrict_to_view)` Get a campaign node for the spectral data browser.
`Campaign[]`	`getCampaigns()` Get all of the campaigns in the database.
`Campaign[]`	`getCampaigns(boolean load_metadata_details)` Get all of the campaigns in the database.
`java.lang.String`	`getCapability(java.lang.String capability)` Get the value of a capability.
`java.util.ArrayList<Category>`	`getCategoriesInfo()` Get the ids and names of all metadata categories.
`java.util.List<spectral_node_object>`	`getChildrenOfNode(spectral_node_object sn)` Get the children of a node of the spectral data browser.
`java.util.List<TaxonomyNodeObject>`	`getChildrenOfTaxonomyNode(TaxonomyNodeObject tn)` Get the children of a node of a taxonomy.
`Country[]`	`getCountries()` Get the list of countries known to the server.
`database_node`	`getDatabaseNode(java.lang.String order_by, boolean restrict_to_view)` Get a database node for the spectral data browser.
`java.lang.Integer`	`getDirectHierarchyId(int spectrum_id)` Get the direct hierarchy id of a single spectrum
`java.util.ArrayList<java.lang.Integer>`	`getDirectHierarchyIds(java.util.ArrayList<java.lang.Integer> spectrum_ids)` Get hierarchy ids, directly above these spectra
`java.util.ArrayList<java.lang.Integer>`	`getDirectSpectrumIdsOfHierarchy(int hierarchy_id)` Get the identifiers of all spectra directly belonging to a hierarchy
`java.util.ArrayList<MetaParameter>`	`getDistinctValuesOfAttribute(int attribute_id)` Get distinct values of an attribute
`ConflictTable`	`getEavMetadataConflicts(int metadata_level, java.util.ArrayList<java.lang.Integer> ids)` Get a conflicts in the EAV metadata for a set of spectra.
`EAVQueryConditionObject`	`getEAVQueryConditionObject(attribute attr)` Return an EAVQueryConditionObject configured for the supplied attribute.
`java.lang.String`	`getEdgeValue(int edge_id)` Get an edge value for a given edge id
`java.lang.Integer`	`getExistingMetaparameterCount(java.lang.Integer attribute_id, java.util.ArrayList<java.lang.Integer> ids)` Get the count of existing metaparameters for the supplied spectrum ids and attribute id
`int`	`getFileFormatId(java.lang.String format)` Get the file format identifier for a file format name.
`Hierarchy`	`getHierarchy(java.lang.Integer hierarchy_id)` Get the hierarchy object for a given hierarchy_id
`java.lang.String`	`getHierarchyFilePath(int hierarchy_id)` Get the file path of a hierarchy.
`int`	`getHierarchyId(Campaign campaign, java.lang.String name, int parent_id)` Get the identifier of a hierarchy node.
`java.util.ArrayList<java.lang.Integer>`	`getHierarchyIdsOfSpectra(java.util.ArrayList<java.lang.Integer> spectrum_ids)` Get a list of hierarchy ids, covering all hierarchies above these spectra
`java.lang.String`	`getHierarchyName(int hierarchy_id)` Get the name of a hierarchy.
`int`	`getHierarchyParentId(int hierarchy_id)` Get the parent_id for a given hierarchy_id
`Institute[]`	`getInstitutes()` Get all of the institutes in the database.
`Instrument`	`getInstrument(Instrument instrument)` Get an instrument that matches the passed object or creates a new instrument and returns it
`Instrument`	`getInstrument(int instrument_id)` Get an instrument.
`CalibrationMetadata[]`	`getInstrumentCalibrationMetadata(int instrument_id)` Get the calibration metadata for an instrument.
`InstrumentDescriptor[]`	`getInstrumentDescriptors()` Get descriptors for all of the instruments in the database.
`Instrument`	`getInstrumentForSpectralFile(SpectralFile spec_file)` Get a instrument object for a given spectral file object.
`java.util.ArrayList<java.lang.Integer>`	`getInstrumentIds(java.util.ArrayList<java.lang.Integer> spectrum_ids)` Get instrument ids for a list of spectra.
`PictureTable`	`getInstrumentPictures(int instrument_id)` Get all of the pictures for an instrument.
`java.util.ArrayList<java.lang.Integer>`	`getIrradiance(java.lang.String campaignId)` Get the identifiers of all spectra that match a full text search.
`User`	`getLoggedInUser()` Get a user object representing the user under which the client is logged in.
`MeasurementUnit`	`getMeasurementUnitFromCoding(int coding)` Get measurement unit for ASD based coding.
`java.util.ArrayList<java.lang.Integer>`	`getMetadataCategoriesForApplicationDomain(int taxonomy_id)` Get the metadata categories for application domain
`ApplicationDomainCategories[]`	`getMetadataCategoriesForApplicationDomains()` Get the metadata categories per application domain
`CategoryTable`	`getMetadataCategoriesForIdAccess(java.lang.String field)` Get the metadata categories for a metadata field, ready for access via ID
`java.util.Hashtable<java.lang.String,java.lang.Integer>`	`getMetadataCategoriesForNameAccess(java.lang.String field)` Get the metadata categories for a metadata field, ready for access via name
`ConflictTable`	`getMetadataConflicts(java.util.ArrayList<java.lang.Integer> spectrum_ids, java.lang.String[] fields)` Get the metadata conflicts for a set of spectra and set of fields.
`MetaParameter`	`getMetaparameter(java.lang.Integer id, java.lang.String attribute_name)` Get metaparameter for spectrum id and EAV attribute
`java.util.ArrayList<java.util.ArrayList<MetaParameter>>`	`getMetaparameters(java.util.ArrayList<java.lang.Integer> ids, java.util.ArrayList<java.lang.Integer> attribute_ids)` Get list of metaparameters for spectrum ids and EAV attributes
`java.util.ArrayList<MetaParameter>`	`getMetaparameters(java.util.ArrayList<java.lang.Integer> ids, java.lang.String attribute_name)` Get metaparameters for spectrum ids and EAV attribute
`java.util.ArrayList<MetaParameter>`	`getMetaparameters(java.util.ArrayList<java.lang.Integer> ids, java.lang.String attribute_name, java.lang.Boolean distinct)` Get metaparameters for spectrum ids and EAV attribute
`MetaparameterStatistics`	`getMetaparameterStatistics(java.util.ArrayList<java.lang.Integer> ids, java.lang.String attribute_name)` Get metaparameter value statistics for spectrum ids and EAV attribute
`MatlabAdaptedArrayList<java.lang.Object>`	`getMetaparameterValues(java.util.ArrayList<java.lang.Integer> ids, java.lang.String attribute_name)` Get values for spectrum ids and EAV attribute (non-distinct values by default)
`MatlabAdaptedArrayList<java.lang.Object>`	`getMetaparameterValues(java.util.ArrayList<java.lang.Integer> ids, java.lang.String attribute_name, java.lang.Boolean distinct)` Get values for spectrum ids and EAV attribute
`java.util.ArrayList<java.lang.Integer>`	`getNewestSpectra(int number_of_spectra)` Get newest N spectra.
`java.util.ArrayList<attribute>`	`getNonNullAttributes(java.util.ArrayList<java.lang.Integer> spectrumIds)`
`java.util.ArrayList<Category>`	`getNonNullCategories(java.util.ArrayList<java.lang.Integer> spectrumIds)` Get the ids and names of all metadata categories used by a set of given spectra.
`java.lang.String[]`	`getPoliciesForSpace(Space space)` Get the data usage policies for a space.
`Query`	`getQueryObject()` Get an empty query object
`Reference`	`getReference(int reference_id)` Get a reference.
`ReferenceBrand[]`	`getReferenceBrands()` Get all of the reference brands in the database.
`CalibrationMetadata[]`	`getReferenceCalibrationMetadata(int reference_id)` Get the calibration metadata for a reference.
`ReferenceDescriptor[]`	`getReferenceDescriptors()` Get descriptors for all of the references in the database.
`PictureTable`	`getReferencePictures(int reference_id)` Get all of the pictures associated with a reference.
`ReferenceSpaceStruct`	`getReferenceSpace(java.util.ArrayList<java.lang.Integer> input_ids)` Get a reference space.
`Sensor[]`	`getSensors()` Get all of the sensors in the database.
`GonioSamplingPoints`	`getSensorSamplingGeometry(SpectralSpace space)` Get sensor sampling geometry
`SPECCHIOServerDescriptor`	`getServerDescriptor()` Get a server descriptor that describes the server to which this client is connected.
`Space[]`	`getSpaces(java.util.ArrayList<java.lang.Integer> ids, boolean split_spaces_by_sensor, boolean split_spaces_by_sensor_and_unit, java.lang.String order_by)` Get the space objects for a set of spectrum identifiers.
`Space[]`	`getSpaces(java.util.ArrayList<java.lang.Integer> ids, java.lang.String order_by)` Get the space objects for a set of spectrum identifiers.
`Spectrum`	`getSpectrum(int spectrum_id, boolean load_metadata)` Get a spectrum.
`Space[]`	`getSpectrumCalibrationSpaces(java.util.ArrayList<java.lang.Integer> spectrum_ids)` Get the calibration spaces for a set of spectra.
`int`	`getSpectrumCountInDB()` Get the number of spectra in the database
`SpectrumFactorTable`	`getSpectrumFactorTable(java.util.ArrayList<java.lang.Integer> spectrum_ids_1, java.util.ArrayList<java.lang.Integer> spectrum_ids_2)` Get the spectrum factor table for a set of spectra.
`java.util.List<java.lang.Integer>`	`getSpectrumIdsForNode(spectral_node_object sn)` Get the identifiers of all spectra beneath a given node of the spectral data browser
`java.util.ArrayList<java.lang.Integer>`	`getSpectrumIdsMatchingFullTextSearch(java.lang.String search_str)` Get the identifiers of all spectra that match a full text search.
`java.util.ArrayList<java.lang.Integer>`	`getSpectrumIdsMatchingFullTextSearchUsingHierarchy(java.lang.String search_str)` Get the identifiers of all spectra that match a full text search using hierarchy.
`java.util.ArrayList<java.lang.Integer>`	`getSpectrumIdsMatchingQuery(Query query)` Get the spectrum identifiers that match a given query.
`PictureTable`	`getSpectrumPictures(int spectrum_id)` Get the pictures associated with a spectrum.
`int`	`getSpectrumQueryCount(Query query)` Get the number of spectra that match a given query.
`int`	`getSubHierarchyId(Campaign campaign, java.lang.String name, int parent_id)` Get the identifier of a sub-hierarchy with a given name, creating the hierarchy if it doesn't exist (deprecated)
`int`	`getSubHierarchyId(java.lang.String name, int parent_id)` Get the identifier of a sub-hierarchy with a given name, creating the hierarchy if it doesn't exist.
`SpectrumDataLink[]`	`getTargetReferenceLinks(java.util.ArrayList<java.lang.Integer> target_ids, java.util.ArrayList<java.lang.Integer> reference_ids)` Get the spectrum data links that refer to a given set of targets and/or references.
`java.util.Hashtable<java.lang.String,java.lang.Integer>`	`getTaxonomyHash(attribute attribute)` Get the taxonomy hash for a given taxonomy
`java.util.Hashtable<java.lang.String,java.lang.Integer>`	`getTaxonomyHash(int attribute_id)` Get the taxonomy hash for a given taxonomy
`int`	`getTaxonomyId(int attribute_id, java.lang.String name)` Get the id for a given taxonomy node in a given taxonomy
`java.util.Hashtable<java.lang.Integer,java.lang.String>`	`getTaxonomyIdToNameHash(int attribute_id)` Get the ID to name hash for a given taxonomy
`TaxonomyNodeObject`	`getTaxonomyNode(int taxonomy_id)` Get the node for a given taxonomy
`TaxonomyNodeObject`	`getTaxonomyRootNode(int attribute_id)` Get the top node for a given taxonomy
`UncertaintyNode`	`getUncertaintyInstrumentNode(int instrument_node_id)` Get instrument node for a selected instrument id
`UncertaintyNode[]`	`getUncertaintyNodeComponents(int uncertainty_node_id)` Retrieve an uncertainty node.
`UncertaintyNode[]`	`getUncertaintyNodeSubSets(int uncertainty_node_id)` Retrieve uncertainty node subsets.
`UncertaintySet`	`getUncertaintySet(int uncertainty_set_id)` Get details of an uncertainty set
`java.util.ArrayList<java.lang.Integer>`	`getUncertaintySetIds(int spectrum_id)` Get ids of uncertainty sets that contain a spectrum id
`java.util.ArrayList<UncertaintySetSpectraList>`	`getUncertaintySetSpectraLists(java.util.ArrayList<java.lang.Integer> spectrum_ids)` Retrieve uncertainty set ids where spectrum ids can be found
`Space[]`	`getUncertaintySpaces(java.util.ArrayList<java.lang.Integer> spectrum_ids, java.util.ArrayList<java.lang.Integer> uncertainty_set_ids, java.lang.String order_by)` Get the uncertainty spaces for a set of spectra and uncertainty set ids.
`UncertaintyNode`	`getUncertaintySpectrumNode(int spectrum_node_id)` Get spectrum node for a selected spectrum node id
`java.util.ArrayList<java.lang.Integer>`	`getUnprocessedHierarchies(java.lang.String campaignId)` Get the identifiers of all spectra that match a full text search.
`User[]`	`getUsers()` Get a list of all of the users in the database.
`User[]`	`getUsersWithStatistics()` Get a list of all of the users in the database with added user statistics (number of loaded spectra, number of campaigns).
`void`	`importCampaign(int user_id, java.io.InputStream is)` Import a campaign.
`void`	`importCampaign(int user_id, java.lang.String server_filepath)` Import a campaign from a file that is on the Glassfish server (used for bigger files to prevent timeouts)
`int`	`insertCampaign(Campaign campaign)` Insert a new campaign into the database
`int`	`insertClosestTargetReferenceLink(int target_id, java.util.ArrayList<java.lang.Integer> reference_ids)` Insert a target-reference link to closest reference on acquisition timeline
`int`	`insertHierarchy(Campaign campaign, java.lang.String name, int parent_id)` Insert a hierarchy node.
`int`	`insertInstitute(Institute institute)` Insert a new institute into the database
`void`	`insertInstrumentCalibration(Calibration c)` Insert calibration for an instrument.
`void`	`insertInstrumentPicture(Picture picture)` Insert a picture of an instrument into the database.
`int`	`insertNewUncertaintySet(UncertaintySet uc_set)` Insert new uncertainty set
`void`	`insertReferenceCalibration(Calibration c)` Insert calibration for a reference into the database.
`void`	`insertReferencePicture(Picture picture)` Insert a picture associated with a reference into the database.
`SpectralFileInsertResult`	`insertSpectralFile(SpectralFile spec_file)` Insert a spectral file into the database.
`int`	`insertSpectrumSubset(UncertaintySpectrumNode uc_spectrum_node)` Insert a spectrum subset
`int`	`insertTargetReferenceLinks(int target_id, java.util.ArrayList<java.lang.Integer> reference_ids)` Insert a target-reference links.
`int`	`insertUncertaintyInstrumentNode(UncertaintyInstrumentNode instrument_node)` Insert an instrument node into the database.
`int`	`insertUncertaintyNode(UncertaintyInstrumentNode uc_instrument_node, int uc_set_id)` Insert an uncertainty node
`int`	`insertUncertaintyNode(UncertaintySpectrumNode uc_spectrum_node, int uc_set_id)` Insert an uncertainty node
`boolean`	`instrumentCalibrationExists(Calibration cal)` Test for the existence of a calibration in the database.
`boolean`	`isLoggedInWithRole(java.lang.String roleName)` Test whether or not the client is logged in under a given role.
`MetaParameter`	`loadMetaparameter(int metaparameter_id)` Get the meta-parameter of the given metaparameter identifier.
`void`	`loadSensor(java.io.InputStream is)` Load a sensor definition into the database from an input stream.
`Space`	`loadSpace(Space space)` Load a Space object.
`boolean`	`moveHierarchy(int source_hierarchy_id, int target_parent_hierarchy)` Move a hierarchy to a new parent hierarchy within the same campaign.
`void`	`refreshMetadataCategory(java.lang.String field)` Causes the client to reload data values the specified category upon next request.
`void`	`removeEavMetadata(attribute attr, java.util.ArrayList<java.lang.Integer> spectrum_ids, int metadata_level)` Remove one or more items of EAV metadata for a collection of spectra for a defined attribute.
`void`	`removeEavMetadata(MetaParameter mp)` Remove an item of EAV metadata.
`void`	`removeEavMetadata(MetaParameter mp, java.util.ArrayList<java.lang.Integer> spectrum_ids)` Remove an item of EAV metadata for a collection of spectra.
`void`	`removeSpectralNode(spectral_node_object sn)` Remove the data corresponding to a node of the spectral data browser.
`void`	`removeSpectralNodes(java.util.ArrayList<spectral_node_object> sns)` Remove the data corresponding to a node of the spectral data browser.
`boolean`	`renameHierarchy(int hierarchy_id, java.lang.String name)` Rename a hierarchy in the database and also on the file system if path is accessible.
`void`	`setProgressReport(ProgressReportInterface pr)` Set the progress report interface to which progress made by this client will be reported.
`AVMatchingListCollection`	`sortByAttributes(java.util.ArrayList<java.lang.Integer> spectrum_ids, java.lang.String... attribute_names)` Sort spectra by the values of the specified attributes
`boolean`	`spectralFileExists(SpectralFile spec_file)` Test for the existence of a spectral file in the database.
`boolean[]`	`spectralFilesExist(SpectralFiles spec_files)` Test for the existence of a spectral files in the database.
`java.lang.String`	`submitRDACollection(RDACollectionDescriptor collection_d)` Submit a collection to Research Data Australia.
`void`	`updateCampaign(Campaign campaign)` Update the information about a campaign
`int`	`updateEavMetadata(MetaParameter mp, java.util.ArrayList<java.lang.Integer> spectrum_ids)` Update EAV metadata.
`int`	`updateEavMetadata(MetaParameter mp, java.util.ArrayList<java.lang.Integer> spectrum_ids, MetaParameter mp_old)` Update EAV metadata.
`int`	`updateEavMetadataAnnotation(MetaParameter mp, java.util.ArrayList<java.lang.Integer> spectrum_ids)` Update EAV metadata annotation.
`void`	`updateInstrument(Instrument instrument)` Update an instrument.
`void`	`updateInstrumentCalibrationMetadata(CalibrationMetadata cm)` Update the calibration metadata for an instrument.
`void`	`updateInstrumentPicture(Picture picture)` Update a picture associated with an instrument.
`int`	`updateOrInsertEavMetadata(java.util.ArrayList<Metadata> md, java.util.ArrayList<java.lang.Integer> ids, int campaignId)` Update or insert EAV metadata.
`int`	`updateOrInsertEavMetadata(MetaParameter mp, java.util.ArrayList<java.lang.Integer> spectrum_ids)` Update or insert EAV metadata.
`int`	`updateOrInsertEavMetadata(MetaParameter mp, int spectrum_id)` Update or insert EAV metadata.
`void`	`updateReference(Reference reference)` Update an reference.
`void`	`updateReferenceCalibrationMetadata(CalibrationMetadata cm)` Update the calibration metadata for a reference.
`void`	`updateReferencePicture(Picture picture)` Update a picture associated with a reference.
`void`	`updateSpectraMetadata(java.util.ArrayList<java.lang.Integer> ids, java.lang.String field, int id)` Update the metadata fields for a set of spectra
`void`	`updateSpectrumVector(int spectrum_id, float[] vector)` Update the spectral vector of a spectrum
`void`	`updateSpectrumVectors(java.util.HashMap<java.lang.Integer,double[]> updateMap)` Update the spectral vector of a spectrum
`void`	`updateUser(User user)` Update the information about a user.

- Method Detail
  - connect
```
void connect()
      throws SPECCHIOClientException
```
    Connect to the server.
    
    Throws:
    
    SPECCHIOClientException - could not log in
  - close
```
void close()
    throws SPECCHIOClientException
```
    Close this client
    
    Throws:
    
    SPECCHIOClientException - could not close client
  - copySpectrum
```
int copySpectrum(int spectrum_id,
                 int target_hierarchy_id)
          throws SPECCHIOClientException
```
    Copy a spectrum to a specified hierarchy.
    
    Parameters:
    
    spectrum_id - the spectrum_id of the spectrum to copy
    
    target_hierarchy_id - the hierarchy_id where the copy is to be stored
    
    Returns:
    
    new spectrum id
    
    Throws:
    
    SPECCHIOClientException - could not log in
  - copySpectra
```
java.util.ArrayList<java.lang.Integer> copySpectra(java.util.ArrayList<java.lang.Integer> spectrum_id,
                                                   int target_hierarchy_id,
                                                   int current_hierarchy_id)
                                            throws SPECCHIOClientException
```
    Copy a spectrum to a specified hierarchy.
    
    Parameters:
    
    spectrum_id - the spectrum_id of the spectrum to copy
    
    target_hierarchy_id - the hierarchy_id where the copy is to be stored
    
    Returns:
    
    new spectrum id
    
    Throws:
    
    SPECCHIOClientException - could not log in
  - copyHierarchy
```
int copyHierarchy(int hierarchy_id,
                  int target_hierarchy_id,
                  java.lang.String new_name)
           throws SPECCHIOClientException
```
    Copy a hierarchy to a specified hierarchy with a new name.
    
    Parameters:
    
    hierarchy_id - the hierarchy_id of the hierarchy to copy
    
    target_hierarchy_id - the hierarchy_id where the copy is to be stored
    
    new_name - new name for the copied hierarchy
    
    Returns:
    
    new hierarchy_id
    
    Throws:
    
    SPECCHIOClientException - could not log in
  - clearMetaparameterRedundancyList
```
void clearMetaparameterRedundancyList()
                               throws SPECCHIOClientException
```
    Clears the known metaparameter list held by the server for this user
    
    Throws:
    
    SPECCHIOClientException
  - createUserAccount
```
User createUserAccount(User user)
                throws SPECCHIOClientException
```
    Create a user account.
    
    Parameters:
    
    user - a user object describing the new user account
    
    Returns:
    
    a new user object containing the complete account details
    
    Throws:
    
    SPECCHIOClientException
  - createUserAccountOnCurrentServer
```
User createUserAccountOnCurrentServer(User user)
                               throws SPECCHIOClientException
```
    Create a user account on this specchio server. Only for admin users.
    
    Parameters:
    
    user - a user object describing the new user account
    
    Returns:
    
    a new user object containing the complete account details
    
    Throws:
    
    SPECCHIOClientException
  - createInstrument
```
void createInstrument(java.lang.String name)
               throws SPECCHIOClientException
```
    Create a new instrument.
    
    Parameters:
    
    name - the name of the new instrument
    
    Throws:
    
    SPECCHIOClientException
  - createReference
```
void createReference(java.lang.String name)
              throws SPECCHIOClientException
```
    Create a new reference.
    
    Parameters:
    
    name - the name of the new reference
    
    Throws:
    
    SPECCHIOClientException
  - dbUpgrade
```
void dbUpgrade(double version,
               java.io.FileInputStream fis)
        throws SPECCHIOClientException
```
    Database upgrade
    
    Parameters:
    
    version - DB version to be upgraded to
    
    fis - File input stream with SQL upgrade statements
    
    Throws:
    
    SPECCHIOClientException
  - deleteCalibration
```
void deleteCalibration(int calibration_id)
                throws SPECCHIOClientException
```
    Delete calibration data from the database
    
    Parameters:
    
    calibration_id - the calibration identifier
    
    Throws:
    
    SPECCHIOClientException
  - deleteInstrument
```
void deleteInstrument(int instrument_id)
               throws SPECCHIOClientException
```
    Delete an instrument from the database.
    
    Parameters:
    
    instrument_id - the instrument identifier
    
    Throws:
    
    SPECCHIOClientException
  - deleteInstrumentPicture
```
void deleteInstrumentPicture(int picture_id)
                      throws SPECCHIOClientException
```
    Delete a picture of an instrument from the database.
    
    Parameters:
    
    picture_id - the picture identifier
    
    Throws:
    
    SPECCHIOClientException
  - deleteReference
```
void deleteReference(int reference_id)
              throws SPECCHIOClientException
```
    Delete a reference from the database.
    
    Parameters:
    
    reference_id - the reference identifier
    
    Throws:
    
    SPECCHIOClientException
  - deleteReferencePicture
```
void deleteReferencePicture(int picture_id)
                     throws SPECCHIOClientException
```
    Delete a picture of a reference from the database.
    
    Parameters:
    
    picture_id - the picture identifier
    
    Throws:
    
    SPECCHIOClientException
  - deleteTargetReferenceLinks
```
int deleteTargetReferenceLinks(int eav_id)
                        throws SPECCHIOClientException
```
    Delete target-reference links from the database.
    
    Parameters:
    
    eav_id - the eav_id identifier
    
    Returns:
    
    the number of links deleted
    
    Throws:
    
    SPECCHIOClientException
  - disconnect
```
void disconnect()
         throws SPECCHIOClientException
```
    Disconnect from the server.
    
    Throws:
    
    SPECCHIOClientException
  - filterSpectrumIdsByHavingAttribute
```
java.util.ArrayList<java.lang.Integer> filterSpectrumIdsByHavingAttribute(java.util.ArrayList<java.lang.Integer> spectrum_ids,
                                                                          java.lang.String attribute_name)
                                                                   throws SPECCHIOClientException
```
    Get the spectrum identifiers that do have a reference to the specified attribute.
    
    Parameters:
    
    spectrum_ids - list of ids to filter
    
    attribute_name - attribute name to filter with
    
    Returns:
    
    an array list of spectrum identifiers that match the filter
    
    Throws:
    
    SPECCHIOClientException
  - filterSpectrumIdsByNotHavingAttribute
```
java.util.ArrayList<java.lang.Integer> filterSpectrumIdsByNotHavingAttribute(java.util.ArrayList<java.lang.Integer> spectrum_ids,
                                                                             java.lang.String attribute_name)
                                                                      throws SPECCHIOClientException
```
    Get the spectrum identifiers that do not have a reference to the specified attribute.
    
    Parameters:
    
    spectrum_ids - list of ids to filter
    
    attribute_name - attribute name to filter with
    
    Returns:
    
    an array list of spectrum identifiers that match the filter
    
    Throws:
    
    SPECCHIOClientException
  - filterSpectrumIdsByHavingAttributeValue
```
java.util.ArrayList<java.lang.Integer> filterSpectrumIdsByHavingAttributeValue(java.util.ArrayList<java.lang.Integer> spectrum_ids,
                                                                               java.lang.String attribute_name,
                                                                               java.lang.Object value)
                                                                        throws SPECCHIOClientException
```
    Get the spectrum identifiers that do reference to the specified attribute of a specified value.
    
    Parameters:
    
    spectrum_ids - list of ids to filter
    
    attribute_name - attribute name to filter with
    
    value - attribute value to match
    
    Returns:
    
    an array list of spectrum identifiers that match the filter
    
    Throws:
    
    SPECCHIOClientException
  - getMetadataCategoriesForApplicationDomains
```
ApplicationDomainCategories[] getMetadataCategoriesForApplicationDomains()
```
    Get the metadata categories per application domain
    
    Returns:
    
    an array of ApplicationDomainCategories object, or null if the information does not exist
  - getAttributesForCategory
```
attribute[] getAttributesForCategory(java.lang.String category)
                              throws SPECCHIOClientException
```
    Get the attributes for a metadata category.
    
    Parameters:
    
    category - the category name
    
    Returns:
    
    an array of attribute objects
    
    Throws:
    
    SPECCHIOClientException
  - getAttributes
```
attribute[] getAttributes()
                   throws SPECCHIOClientException
```
    Get the attributes object containing information on all attributes, units and categories.
    
    Returns:
    
    Attributes
    
    Throws:
    
    SPECCHIOClientException
  - getAttributesIdHash
```
java.util.Hashtable<java.lang.Integer,attribute> getAttributesIdHash()
                                                              throws SPECCHIOClientException
```
    Get the attributes hashtable
    
    Returns:
    
    Attributes stored in hashtable, indexed by attribute_id
    
    Throws:
    
    SPECCHIOClientException
  - getAttributesNameHash
```
java.util.Hashtable<java.lang.String,attribute> getAttributesNameHash()
                                                               throws SPECCHIOClientException
```
    Get the attributes hashtable
    
    Returns:
    
    Attributes stored in hashtable, indexed by attribute name
    
    Throws:
    
    SPECCHIOClientException
  - getAttributeUnits
```
Units getAttributeUnits(attribute attr)
                 throws SPECCHIOClientException
```
    Get the units for an attribute.
    
    Parameters:
    
    attr - the attribute
    
    Returns:
    
    a units object representing the attribute's units
    
    Throws:
    
    SPECCHIOClientException
  - getCampaign
```
Campaign getCampaign(int campaign_id)
              throws SPECCHIOClientException
```
    Get a campaign descriptor.
    
    Parameters:
    
    campaign_id - the campaign identifier
    
    Returns:
    
    a new campaign object
    
    Throws:
    
    SPECCHIOClientException
  - getCategoriesInfo
```
java.util.ArrayList<Category> getCategoriesInfo()
                                         throws SPECCHIOClientException
```
    Get the ids and names of all metadata categories.
    
    Returns:
    
    an array list of category information
    
    Throws:
    
    SPECCHIOClientException
  - getNonNullCategories
```
java.util.ArrayList<Category> getNonNullCategories(java.util.ArrayList<java.lang.Integer> spectrumIds)
```
    Get the ids and names of all metadata categories used by a set of given spectra.
    
    Parameters:
    
    spectrumIds - list of spectrum ids for which to search used categories
    
    Returns:
    
    an array list of category information
  - getNonNullAttributes
```
java.util.ArrayList<attribute> getNonNullAttributes(java.util.ArrayList<java.lang.Integer> spectrumIds)
```
  - findMatchingSpectra
```
java.util.ArrayList<java.lang.Integer> findMatchingSpectra(java.util.ArrayList<java.lang.Integer> spectrumIds,
                                                           java.util.ArrayList<QueryAttribute> queryAttributes)
```
  - createFilterCollection
```
void createFilterCollection(java.util.ArrayList<java.lang.Integer> specturmIds,
                            java.util.ArrayList<java.lang.Integer> attributeIds)
```
  - getCampaignExportInputStream
```
java.io.InputStream getCampaignExportInputStream(Campaign c)
                                          throws SPECCHIOClientException
```
    Export a campaign.
    
    Parameters:
    
    c - the campaign to be exported
    
    Returns:
    
    an input stream connected to the exported campaign date
    
    Throws:
    
    SPECCHIOClientException
  - getCampaignNode
```
campaign_node getCampaignNode(int campaign_id,
                              java.lang.String order_by,
                              boolean restrict_to_view)
                       throws SPECCHIOClientException
```
    Get a campaign node for the spectral data browser.
    
    Parameters:
    
    campaign_id - the campaign identifier
    
    order_by - the attribute by which to order the campaign's descendents
    
    restrict_to_view - show user's data only
    
    Returns:
    
    a new campaign node object, or null if the campaign does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getCampaigns
```
Campaign[] getCampaigns()
                 throws SPECCHIOClientException
```
    Get all of the campaigns in the database.
    
    Returns:
    
    an array of campaign objects descriving each campaign in the database
    
    Throws:
    
    SPECCHIOClientException
  - getCampaigns
```
Campaign[] getCampaigns(boolean load_metadata_details)
                 throws SPECCHIOWebClientException
```
    Get all of the campaigns in the database.
    
    Parameters:
    
    load_metadata_details - defines if additional detailed metadata should be loaded
    
    Returns:
    
    an array of campaign objects describing each campaign in the database
    
    Throws:
    
    SPECCHIOWebClientException
  - getCalibrationIds
```
java.util.ArrayList<java.lang.Integer> getCalibrationIds(java.util.ArrayList<java.lang.Integer> spectrum_ids)
                                                  throws SPECCHIOWebClientException
```
    Get calibration ids for a list of spectra.
    
    Parameters:
    
    spectrum_ids - the spectrum identifiers
    
    Returns:
    
    list of calibration ids, zero where no calibration is defined
    
    Throws:
    
    SPECCHIOWebClientException
  - getCalibratedInstrument
```
Instrument getCalibratedInstrument(int calibration_id)
                            throws SPECCHIOClientException
```
    Get a calibrated instrument.
    
    Parameters:
    
    calibration_id - the calibration identifier
    
    Returns:
    
    a new Instrument object, or null if the calibrated instrument does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getCalibrationMetadataByCalibrationNumber
```
CalibrationMetadata[] getCalibrationMetadataByCalibrationNumber(int instrument_id,
                                                                int calibration_number)
                                                         throws SPECCHIOClientException
```
    Get an array of CalibrationMetadata based on an instrument id and a calibration number (typically an ASD instrument).
    
    Parameters:
    
    instrument_id - the instrument_id
    
    calibration_number - the calibration number is given in the Metadata field "Calibration Number"
    
    Returns:
    
    an array of CalibrationMetadata
    
    Throws:
    
    SPECCHIOClientException
  - getCapability
```
java.lang.String getCapability(java.lang.String capability)
                        throws SPECCHIOClientException
```
    Get the value of a capability.
    
    Parameters:
    
    capability - the capability name
    
    Returns:
    
    the value of the capability, or null if the capability is not recognised
    
    Throws:
    
    SPECCHIOClientException
  - getChildrenOfNode
```
java.util.List<spectral_node_object> getChildrenOfNode(spectral_node_object sn)
                                                throws SPECCHIOClientException
```
    Get the children of a node of the spectral data browser.
    
    Parameters:
    
    sn - the node
    
    Returns:
    
    a list of the node's children
    
    Throws:
    
    SPECCHIOClientException
  - getChildrenOfTaxonomyNode
```
java.util.List<TaxonomyNodeObject> getChildrenOfTaxonomyNode(TaxonomyNodeObject tn)
                                                      throws SPECCHIOClientException
```
    Get the children of a node of a taxonomy.
    
    Parameters:
    
    tn - the node
    
    Returns:
    
    a list of the node's children
    
    Throws:
    
    SPECCHIOClientException
  - getCountries
```
Country[] getCountries()
                throws SPECCHIOClientException
```
    Get the list of countries known to the server.
    
    Returns:
    
    an array of Country objects
    
    Throws:
    
    SPECCHIOClientException
  - getDatabaseNode
```
database_node getDatabaseNode(java.lang.String order_by,
                              boolean restrict_to_view)
                       throws SPECCHIOClientException
```
    Get a database node for the spectral data browser.
    
    Parameters:
    
    order_by - the attribute to order by
    
    restrict_to_view - display the current user's data only
    
    Returns:
    
    a database_node object
    
    Throws:
    
    SPECCHIOClientException
  - getDirectHierarchyId
```
java.lang.Integer getDirectHierarchyId(int spectrum_id)
                                throws SPECCHIOClientException
```
    Get the direct hierarchy id of a single spectrum
    
    Parameters:
    
    spectrum_id - the identifier of the spectrum
    
    Returns:
    
    hierarchy id
    
    Throws:
    
    SPECCHIOClientException
  - getDirectHierarchyIds
```
java.util.ArrayList<java.lang.Integer> getDirectHierarchyIds(java.util.ArrayList<java.lang.Integer> spectrum_ids)
                                                      throws SPECCHIOClientException
```
    Get hierarchy ids, directly above these spectra
    
    Parameters:
    
    spectrum_ids - the identifiers of the desired spectra
    
    Returns:
    
    hierarchy ids
    
    Throws:
    
    SPECCHIOClientException
  - getDistinctValuesOfAttribute
```
java.util.ArrayList<MetaParameter> getDistinctValuesOfAttribute(int attribute_id)
                                                         throws SPECCHIOClientException
```
    Get distinct values of an attribute
    
    Parameters:
    
    attribute_id - id of the required attribute
    
    Returns:
    
    arraylist of metaparameters
    
    Throws:
    
    SPECCHIOClientException
  - getEavMetadataConflicts
```
ConflictTable getEavMetadataConflicts(int metadata_level,
                                      java.util.ArrayList<java.lang.Integer> ids)
                               throws SPECCHIOClientException
```
    Get a conflicts in the EAV metadata for a set of spectra.
    
    Parameters:
    
    metadata_level - storage level identifier
    
    ids - the primary entity identifiers
    
    Returns:
    
    a ConflictTable object containing all of the conflicts
    
    Throws:
    
    SPECCHIOClientException
  - getEAVQueryConditionObject
```
EAVQueryConditionObject getEAVQueryConditionObject(attribute attr)
```
    Return an EAVQueryConditionObject configured for the supplied attribute.
    
    Parameters:
    
    attr - attribute object
    
    Returns:
  - getExistingMetaparameterCount
```
java.lang.Integer getExistingMetaparameterCount(java.lang.Integer attribute_id,
                                                java.util.ArrayList<java.lang.Integer> ids)
                                         throws SPECCHIOClientException
```
    Get the count of existing metaparameters for the supplied spectrum ids and attribute id
    
    Parameters:
    
    attribute_id - id of the attribute
    
    ids - spectrum ids
    
    Returns:
    
    Integer
    
    Throws:
    
    SPECCHIOClientException
  - getFileFormatId
```
int getFileFormatId(java.lang.String format)
             throws SPECCHIOClientException
```
    Get the file format identifier for a file format name.
    
    Parameters:
    
    format - the file format name
    
    Returns:
    
    the identifier associated with the specified file format, or -1 if file format is not recognised
    
    Throws:
    
    SPECCHIOClientException
  - getHierarchy
```
Hierarchy getHierarchy(java.lang.Integer hierarchy_id)
                throws SPECCHIOWebClientException
```
    Get the hierarchy object for a given hierarchy_id
    
    Parameters:
    
    hierarchy_id - the hierarchy_id identifying the required node
    
    Returns:
    
    the hierarchy object, or -1 if the node does not exist
    
    Throws:
    
    SPECCHIOWebClientException
  - getHierarchyId
```
int getHierarchyId(Campaign campaign,
                   java.lang.String name,
                   int parent_id)
            throws SPECCHIOClientException
```
    Get the identifier of a hierarchy node.
    
    Parameters:
    
    campaign - the campaign in which the node is located
    
    name - the name of the node
    
    parent_id - the parent of the node
    
    Returns:
    
    the identifier of the child of parent_id with the given name, or -1 if the node does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getHierarchyIdsOfSpectra
```
java.util.ArrayList<java.lang.Integer> getHierarchyIdsOfSpectra(java.util.ArrayList<java.lang.Integer> spectrum_ids)
                                                         throws SPECCHIOClientException
```
    Get a list of hierarchy ids, covering all hierarchies above these spectra
    
    Parameters:
    
    spectrum_ids - the identifiers of the desired spectra
    
    Returns:
    
    hierarchy ids
    
    Throws:
    
    SPECCHIOClientException
  - getHierarchyParentId
```
int getHierarchyParentId(int hierarchy_id)
                  throws SPECCHIOClientException
```
    Get the parent_id for a given hierarchy_id
    
    Parameters:
    
    hierarchy_id - the hierarchy_id identifying the required node
    
    Returns:
    
    id of the parent of given hierarchy
    
    Throws:
    
    SPECCHIOClientException
  - getHierarchyFilePath
```
java.lang.String getHierarchyFilePath(int hierarchy_id)
                               throws SPECCHIOClientException
```
    Get the file path of a hierarchy.
    
    Parameters:
    
    hierarchy_id - the identifier of the hierarchy
    
    Throws:
    
    SPECCHIOClientException - the database could not accessed
  - getHierarchyName
```
java.lang.String getHierarchyName(int hierarchy_id)
                           throws SPECCHIOClientException
```
    Get the name of a hierarchy.
    
    Parameters:
    
    hierarchy_id - the identifier of the hierarchy
    
    Throws:
    
    SPECCHIOClientException - the database could not accessed
  - getInstitutes
```
Institute[] getInstitutes()
                   throws SPECCHIOClientException
```
    Get all of the institutes in the database.
    
    Throws:
    
    SPECCHIOClientException
  - getInstrument
```
Instrument getInstrument(int instrument_id)
                  throws SPECCHIOClientException
```
    Get an instrument.
    
    Parameters:
    
    instrument_id - the instrument identifier
    
    Returns:
    
    a new Instrument object, or null if the instrument does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getInstrument
```
Instrument getInstrument(Instrument instrument)
                  throws SPECCHIOWebClientException
```
    Get an instrument that matches the passed object or creates a new instrument and returns it
    
    Parameters:
    
    instrument - instance
    
    Returns:
    
    a new Instrument object
    
    Throws:
    
    SPECCHIOWebClientException
  - getInstrumentIds
```
java.util.ArrayList<java.lang.Integer> getInstrumentIds(java.util.ArrayList<java.lang.Integer> spectrum_ids)
                                                 throws SPECCHIOWebClientException
```
    Get instrument ids for a list of spectra.
    
    Parameters:
    
    spectrum_ids - the spectrum identifiers
    
    Returns:
    
    list of instrument ids, zero where no instrument is defined
    
    Throws:
    
    SPECCHIOWebClientException
  - getInstrumentCalibrationMetadata
```
CalibrationMetadata[] getInstrumentCalibrationMetadata(int instrument_id)
                                                throws SPECCHIOClientException
```
    Get the calibration metadata for an instrument.
    
    Parameters:
    
    instrument_id - the instrument identifier
    
    Returns:
    
    an array of CalibrationMetadata objects, or null if the instrument does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getInstrumentDescriptors
```
InstrumentDescriptor[] getInstrumentDescriptors()
                                         throws SPECCHIOClientException
```
    Get descriptors for all of the instruments in the database.
    
    Returns:
    
    an array of InstrumentDescriptor objects
    
    Throws:
    
    SPECCHIOClientException
  - getInstrumentForSpectralFile
```
Instrument getInstrumentForSpectralFile(SpectralFile spec_file)
                                 throws SPECCHIOClientException
```
    Get a instrument object for a given spectral file object.
    
    Parameters:
    
    spec_file - the spectral file
    
    Returns:
    
    a new Instrument object
    
    Throws:
    
    SPECCHIOClientException
  - getInstrumentPictures
```
PictureTable getInstrumentPictures(int instrument_id)
                            throws SPECCHIOClientException
```
    Get all of the pictures for an instrument.
    
    Parameters:
    
    instrument_id - the instrument identifier
    
    Returns:
    
    a PictureTable object containing all of the pictures for this instrument, or null if the instrument doesn't exist
    
    Throws:
    
    SPECCHIOClientException
  - getLoggedInUser
```
User getLoggedInUser()
```
    Get a user object representing the user under which the client is logged in.
    
    Returns:
    
    a reference to a user object, or null if the client is not connected
  - getMetadataCategoriesForApplicationDomain
```
java.util.ArrayList<java.lang.Integer> getMetadataCategoriesForApplicationDomain(int taxonomy_id)
                                                                          throws SPECCHIOClientException
```
    Get the metadata categories for application domain
    
    Parameters:
    
    taxonomy_id - the field name
    
    Returns:
    
    a ArrayList object, or null if the field does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getMetadataCategoriesForIdAccess
```
CategoryTable getMetadataCategoriesForIdAccess(java.lang.String field)
                                        throws SPECCHIOClientException
```
    Get the metadata categories for a metadata field, ready for access via ID
    
    Parameters:
    
    field - the field name
    
    Returns:
    
    a CategoryTable object, or null if the field does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getMetadataCategoriesForNameAccess
```
java.util.Hashtable<java.lang.String,java.lang.Integer> getMetadataCategoriesForNameAccess(java.lang.String field)
                                                                                    throws SPECCHIOClientException
```
    Get the metadata categories for a metadata field, ready for access via name
    
    Parameters:
    
    field - the field name
    
    Returns:
    
    a CategoryTable object, or null if the field does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getMetaparameters
```
java.util.ArrayList<MetaParameter> getMetaparameters(java.util.ArrayList<java.lang.Integer> ids,
                                                     java.lang.String attribute_name)
                                              throws SPECCHIOClientException
```
    Get metaparameters for spectrum ids and EAV attribute
    
    Parameters:
    
    ids - spectrum ids
    
    attribute_name - attribute name
    
    Returns:
    
    list of metaparameters, or null if the field does not exist
    
    Throws:
    
    SPECCHIOClientException
  - calculateSunAngle
```
void calculateSunAngle(java.util.ArrayList<java.lang.Integer> spectrumIds,
                       SPECCHIOClient client)
                throws SPECCHIOClientException
```
    Get metaparameters for spectrum ids and EAV attribute
    
    Parameters:
    
    spectrumIds - spectrum ids
    
    Throws:
    
    SPECCHIOClientException
  - getMetaparameter
```
MetaParameter getMetaparameter(java.lang.Integer id,
                               java.lang.String attribute_name)
                        throws SPECCHIOWebClientException
```
    Get metaparameter for spectrum id and EAV attribute
    
    Parameters:
    
    id - spectrum id
    
    attribute_name - attribute name
    
    Returns:
    
    metaparameter, or null if the field does not exist
    
    Throws:
    
    SPECCHIOWebClientException
  - getMetaparameters
```
java.util.ArrayList<java.util.ArrayList<MetaParameter>> getMetaparameters(java.util.ArrayList<java.lang.Integer> ids,
                                                                          java.util.ArrayList<java.lang.Integer> attribute_ids)
                                                                   throws SPECCHIOWebClientException
```
    Get list of metaparameters for spectrum ids and EAV attributes
    
    Parameters:
    
    ids - spectrum ids
    
    attribute_ids - list of attribute ids
    
    Returns:
    
    list of list of metaparameters, or null if the field does not exist
    
    Throws:
    
    SPECCHIOWebClientException
  - getMetaparameters
```
java.util.ArrayList<MetaParameter> getMetaparameters(java.util.ArrayList<java.lang.Integer> ids,
                                                     java.lang.String attribute_name,
                                                     java.lang.Boolean distinct)
                                              throws SPECCHIOWebClientException
```
    Get metaparameters for spectrum ids and EAV attribute
    
    Parameters:
    
    ids - spectrum ids
    
    attribute_name - attribute name
    
    distinct - defines if distinct values should be returned or repeated values for the given spectrum ids: distinct = false means parameters for all spectra, even if redundant
    
    Returns:
    
    list of metaparameters, or null if the field does not exist
    
    Throws:
    
    SPECCHIOWebClientException
  - getMetaparameterStatistics
```
MetaparameterStatistics getMetaparameterStatistics(java.util.ArrayList<java.lang.Integer> ids,
                                                   java.lang.String attribute_name)
                                            throws SPECCHIOWebClientException
```
    Get metaparameter value statistics for spectrum ids and EAV attribute
    
    Parameters:
    
    ids - spectrum ids
    
    attribute_name - attribute name
    
    Returns:
    
    structure with Metaparameter holding statistic values
    
    Throws:
    
    SPECCHIOWebClientException
  - getMetaparameterValues
```
MatlabAdaptedArrayList<java.lang.Object> getMetaparameterValues(java.util.ArrayList<java.lang.Integer> ids,
                                                                java.lang.String attribute_name)
                                                         throws SPECCHIOWebClientException
```
    Get values for spectrum ids and EAV attribute (non-distinct values by default)
    
    Parameters:
    
    ids - spectrum ids
    
    attribute_name - attribute name
    
    Returns:
    
    list of values, or null if the field does not exist
    
    Throws:
    
    SPECCHIOWebClientException
  - getMetaparameterValues
```
MatlabAdaptedArrayList<java.lang.Object> getMetaparameterValues(java.util.ArrayList<java.lang.Integer> ids,
                                                                java.lang.String attribute_name,
                                                                java.lang.Boolean distinct)
                                                         throws SPECCHIOWebClientException
```
    Get values for spectrum ids and EAV attribute
    
    Parameters:
    
    ids - spectrum ids
    
    attribute_name - attribute name
    
    distinct - defines if distinct values should be returned or repeated values for the given spectrum ids
    
    Returns:
    
    list of values, or null if the field does not exist
    
    Throws:
    
    SPECCHIOWebClientException
  - getMetadataConflicts
```
ConflictTable getMetadataConflicts(java.util.ArrayList<java.lang.Integer> spectrum_ids,
                                   java.lang.String[] fields)
                            throws SPECCHIOClientException
```
    Get the metadata conflicts for a set of spectra and set of fields.
    
    Parameters:
    
    spectrum_ids - the spectrum identifiers
    
    fields - the fields to check
    
    Returns:
    
    a ConflictTable object listing the conflicts found
    
    Throws:
    
    SPECCHIOClientException
  - getMeasurementUnitFromCoding
```
MeasurementUnit getMeasurementUnitFromCoding(int coding)
                                      throws SPECCHIOWebClientException
```
    Get measurement unit for ASD based coding.
    
    Parameters:
    
    coding - coding based on ASD coding
    
    Returns:
    
    a new MeasurementUnit object, or null if the coding does not exist
    
    Throws:
    
    SPECCHIOWebClientException
  - getNewestSpectra
```
java.util.ArrayList<java.lang.Integer> getNewestSpectra(int number_of_spectra)
                                                 throws SPECCHIOWebClientException
```
    Get newest N spectra.
    
    Parameters:
    
    number_of_spectra -
    
    Returns:
    
    list of spectrum ids ordered by data ingestion time
    
    Throws:
    
    SPECCHIOWebClientException
  - getPoliciesForSpace
```
java.lang.String[] getPoliciesForSpace(Space space)
                                throws SPECCHIOClientException
```
    Get the data usage policies for a space.
    
    Parameters:
    
    space - the space
    
    Returns:
    
    an array of Policy objects
    
    Throws:
    
    SPECCHIOClientException
  - getQueryObject
```
Query getQueryObject()
              throws SPECCHIOClientException
```
    Get an empty query object
    
    Returns:
    
    a Query Object
    
    Throws:
    
    SPECCHIOClientException
  - getReference
```
Reference getReference(int reference_id)
                throws SPECCHIOClientException
```
    Get a reference.
    
    Parameters:
    
    reference_id - the reference identifier
    
    Returns:
    
    a new Reference object, or null if the instrument does not exist
    
    Throws:
    
    SPECCHIOClientException
  - getReferenceCalibrationMetadata
```
CalibrationMetadata[] getReferenceCalibrationMetadata(int reference_id)
                                               throws SPECCHIOClientException
```
    Get the calibration metadata for a reference.
    
    Parameters:
    
    reference_id - the reference identifier
    
    Returns:
    
    an array of CalibrationMetadata objects, or null if the reference does note exist
    
    Throws:
    
    SPECCHIOClientException
  - getReferenceDescriptors
```
ReferenceDescriptor[] getReferenceDescriptors()
                                       throws SPECCHIOClientException
```
    Get descriptors for all of the references in the database.
    
    Returns:
    
    an arra of ReferenceDescriptor objects
    
    Throws:
    
    SPECCHIOClientException
  - getReferenceBrands
```
ReferenceBrand[] getReferenceBrands()
                             throws SPECCHIOClientException
```
    Get all of the reference brands in the database.
    
    Returns:
    
    an array of ReferenceBrand objects
    
    Throws:
    
    SPECCHIOClientException
  - getReferencePictures
```
PictureTable getReferencePictures(int reference_id)
                           throws SPECCHIOClientException
```
    Get all of the pictures associated with a reference.
    
    Parameters:
    
    reference_id - the reference identifier
    
    Returns:
    
    a PictureTable containing all of the pictures
    
    Throws:
    
    SPECCHIOClientException
  - getReferenceSpace
```
ReferenceSpaceStruct getReferenceSpace(java.util.ArrayList<java.lang.Integer> input_ids)
                                throws SPECCHIOClientException
```
    Get a reference space.
    
    Parameters:
    
    input_ids -
    
    Returns:
    
    a Space object, or null if no space could be found
    
    Throws:
    
    SPECCHIOClientException
  - getServerDescriptor
```
SPECCHIOServerDescriptor getServerDescriptor()
```
    Get a server descriptor that describes the server to which this client is connected.
    
    Returns:
    
    a new server descriptor object
  - getSensors
```
Sensor[] getSensors()
             throws SPECCHIOClientException
```
    Get all of the sensors in the database.
    
    Returns:
    
    an array of Sensor objects
    
    Throws:
    
    SPECCHIOClientException
  - getSensorSamplingGeometry
```
GonioSamplingPoints getSensorSamplingGeometry(SpectralSpace space)
                                       throws SPECCHIOWebClientException
```
    Get sensor sampling geometry
    
    Parameters:
    
    space - holds spectra ids of which geometry is to retrieved
    
    Returns:
    
    a new GonioSamplingPoints, or null if no geometries were found
    
    Throws:
    
    SPECCHIOWebClientException
  - getSpaces
```
Space[] getSpaces(java.util.ArrayList<java.lang.Integer> ids,
                  boolean split_spaces_by_sensor,
                  boolean split_spaces_by_sensor_and_unit,
                  java.lang.String order_by)
           throws SPECCHIOClientException
```
    Get the space objects for a set of spectrum identifiers.
    
    Parameters:
    
    ids - the spectrum identifiers
    
    split_spaces_by_sensor - boolean
    
    split_spaces_by_sensor_and_unit - boolean
    
    order_by - the field to order by
    
    Throws:
    
    SPECCHIOClientException
  - getSpaces
```
Space[] getSpaces(java.util.ArrayList<java.lang.Integer> ids,
                  java.lang.String order_by)
           throws SPECCHIOWebClientException
```
    Get the space objects for a set of spectrum identifiers. Configured to sort by sensor, unit, instrument and calibration
    
    Parameters:
    
    ids - the spectrum identifiers
    
    order_by - the field to order by
    
    Throws:
    
    SPECCHIOWebClientException
  - getSpectrum
```
Spectrum getSpectrum(int spectrum_id,
                     boolean load_metadata)
              throws SPECCHIOClientException
```
    Get a spectrum.
    
    Parameters:
    
    spectrum_id - the spectrum identifier
    
    load_metadata - load all spectrum metadata?
    
    Returns:
    
    a Spectrum object
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumCountInDB
```
int getSpectrumCountInDB()
                  throws SPECCHIOClientException
```
    Get the number of spectra in the database
    
    Returns:
    
    the number of spectra in the database
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumCalibrationSpaces
```
Space[] getSpectrumCalibrationSpaces(java.util.ArrayList<java.lang.Integer> spectrum_ids)
                              throws SPECCHIOClientException
```
    Get the calibration spaces for a set of spectra.
    
    Parameters:
    
    spectrum_ids - the spectrum identifiers
    
    Returns:
    
    an array of Space objects
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumFactorTable
```
SpectrumFactorTable getSpectrumFactorTable(java.util.ArrayList<java.lang.Integer> spectrum_ids_1,
                                           java.util.ArrayList<java.lang.Integer> spectrum_ids_2)
                                    throws SPECCHIOClientException
```
    Get the spectrum factor table for a set of spectra.
    
    Parameters:
    
    spectrum_ids_1 -
    
    spectrum_ids_2 -
    
    Returns:
    
    a SpectrumFactorTable object
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumIdsForNode
```
java.util.List<java.lang.Integer> getSpectrumIdsForNode(spectral_node_object sn)
                                                 throws SPECCHIOClientException
```
    Get the identifiers of all spectra beneath a given node of the spectral data browser
    
    Parameters:
    
    sn - the node
    
    Returns:
    
    a list of spectrum identifiers
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumIdsMatchingFullTextSearch
```
java.util.ArrayList<java.lang.Integer> getSpectrumIdsMatchingFullTextSearch(java.lang.String search_str)
                                                                     throws SPECCHIOClientException
```
    Get the identifiers of all spectra that match a full text search.
    
    Parameters:
    
    search_str - the search string
    
    Returns:
    
    an array list of spectrum identifiers
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumIdsMatchingFullTextSearchUsingHierarchy
```
java.util.ArrayList<java.lang.Integer> getSpectrumIdsMatchingFullTextSearchUsingHierarchy(java.lang.String search_str)
                                                                                   throws SPECCHIOClientException
```
    Get the identifiers of all spectra that match a full text search using hierarchy.
    
    Parameters:
    
    search_str - the search string
    
    Returns:
    
    an array list of spectrum identifiers
    
    Throws:
    
    SPECCHIOClientException
  - getUnprocessedHierarchies
```
java.util.ArrayList<java.lang.Integer> getUnprocessedHierarchies(java.lang.String campaignId)
                                                          throws SPECCHIOClientException
```
    Get the identifiers of all spectra that match a full text search.
    
    Parameters:
    
    campaignId - the search string
    
    Returns:
    
    an array list of spectrum identifiers
    
    Throws:
    
    SPECCHIOClientException
  - getIrradiance
```
java.util.ArrayList<java.lang.Integer> getIrradiance(java.lang.String campaignId)
                                              throws SPECCHIOClientException
```
    Get the identifiers of all spectra that match a full text search.
    
    Parameters:
    
    campaignId - the search string
    
    Returns:
    
    an array list of spectrum identifiers
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumIdsMatchingQuery
```
java.util.ArrayList<java.lang.Integer> getSpectrumIdsMatchingQuery(Query query)
                                                            throws SPECCHIOClientException
```
    Get the spectrum identifiers that match a given query.
    
    Parameters:
    
    query - the query
    
    Returns:
    
    an array list of spectrum identifiers that match the query
    
    Throws:
    
    SPECCHIOClientException
  - getDirectSpectrumIdsOfHierarchy
```
java.util.ArrayList<java.lang.Integer> getDirectSpectrumIdsOfHierarchy(int hierarchy_id)
                                                                throws SPECCHIOClientException
```
    Get the identifiers of all spectra directly belonging to a hierarchy
    
    Parameters:
    
    hierarchy_id - the hierarchy_id
    
    Returns:
    
    a list of spectrum identifiers
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumPictures
```
PictureTable getSpectrumPictures(int spectrum_id)
                          throws SPECCHIOClientException
```
    Get the pictures associated with a spectrum.
    
    Parameters:
    
    spectrum_id - the spectrum identifier
    
    Returns:
    
    a PictureTable containing all of the pictures associated with the spectrum
    
    Throws:
    
    SPECCHIOClientException
  - getSpectrumQueryCount
```
int getSpectrumQueryCount(Query query)
                   throws SPECCHIOClientException
```
    Get the number of spectra that match a given query.
    
    Parameters:
    
    query - the query
    
    Returns:
    
    the number of spectra that match the query
    
    Throws:
    
    SPECCHIOClientException
  - getTargetReferenceLinks
```
SpectrumDataLink[] getTargetReferenceLinks(java.util.ArrayList<java.lang.Integer> target_ids,
                                           java.util.ArrayList<java.lang.Integer> reference_ids)
                                    throws SPECCHIOClientException
```
    Get the spectrum data links that refer to a given set of targets and/or references.
    
    Parameters:
    
    target_ids - the identifiers of the target spectra (null or empty to match all targets)
    
    reference_ids - the identifiers of the reference spectra (null or empty to match all references)
    
    Throws:
    
    SPECCHIOClientException
  - getSubHierarchyId
```
int getSubHierarchyId(Campaign campaign,
                      java.lang.String name,
                      int parent_id)
               throws SPECCHIOClientException
```
    Get the identifier of a sub-hierarchy with a given name, creating the hierarchy if it doesn't exist (deprecated)
    
    Parameters:
    
    campaign - the campaign into which to insert the hierarchy
    
    parent_id - the identifier of the the parent of the hierarchy
    
    name - the name of the desired hierarchy
    
    Returns:
    
    the identifier of the child of parent_id with the name hierarchy_name
    
    Throws:
    
    SPECCHIOClientException
  - getSubHierarchyId
```
int getSubHierarchyId(java.lang.String name,
                      int parent_id)
               throws SPECCHIOClientException
```
    Get the identifier of a sub-hierarchy with a given name, creating the hierarchy if it doesn't exist.
    
    Parameters:
    
    name - the name of the desired hierarchy
    
    parent_id - the identifier of the the parent of the hierarchy
    
    Returns:
    
    the identifier of the child of parent_id with the name hierarchy_name
    
    Throws:
    
    SPECCHIOClientException
  - getTaxonomyRootNode
```
TaxonomyNodeObject getTaxonomyRootNode(int attribute_id)
                                throws SPECCHIOClientException
```
    Get the top node for a given taxonomy
    
    Parameters:
    
    attribute_id - id of the attribute that defines the taxonomy
    
    Throws:
    
    SPECCHIOClientException
  - getTaxonomyNode
```
TaxonomyNodeObject getTaxonomyNode(int taxonomy_id)
                            throws SPECCHIOClientException
```
    Get the node for a given taxonomy
    
    Parameters:
    
    taxonomy_id - taxonomy_id that defines the taxonomy
    
    Throws:
    
    SPECCHIOClientException
  - getTaxonomyId
```
int getTaxonomyId(int attribute_id,
                  java.lang.String name)
           throws SPECCHIOClientException
```
    Get the id for a given taxonomy node in a given taxonomy
    
    Parameters:
    
    attribute_id - attribute_id that defines the taxonomy
    
    name - name of the node of which the id is required
    
    Throws:
    
    SPECCHIOClientException
  - getTaxonomyHash
```
java.util.Hashtable<java.lang.String,java.lang.Integer> getTaxonomyHash(int attribute_id)
                                                                 throws SPECCHIOClientException
```
    Get the taxonomy hash for a given taxonomy
    
    Parameters:
    
    attribute_id - attribute_id that defines the taxonomy
    
    Throws:
    
    SPECCHIOClientException
  - getTaxonomyHash
```
java.util.Hashtable<java.lang.String,java.lang.Integer> getTaxonomyHash(attribute attribute)
                                                                 throws SPECCHIOClientException
```
    Get the taxonomy hash for a given taxonomy
    
    Parameters:
    
    attribute - attribute that defines the taxonomy
    
    Throws:
    
    SPECCHIOClientException
  - getTaxonomyIdToNameHash
```
java.util.Hashtable<java.lang.Integer,java.lang.String> getTaxonomyIdToNameHash(int attribute_id)
                                                                         throws SPECCHIOClientException
```
    Get the ID to name hash for a given taxonomy
    
    Parameters:
    
    attribute_id - attribute_id that defines the taxonomy
    
    Throws:
    
    SPECCHIOClientException
  - getUncertaintySet
```
UncertaintySet getUncertaintySet(int uncertainty_set_id)
                          throws SPECCHIOClientException
```
    Get details of an uncertainty set
    
    Parameters:
    
    uncertainty_set_id, - the desired uncertainty_set_id of the uncertainty set
    
    Throws:
    
    SPECCHIOClientException
  - getUncertaintySetIds
```
java.util.ArrayList<java.lang.Integer> getUncertaintySetIds(int spectrum_id)
                                                     throws SPECCHIOClientException
```
    Get ids of uncertainty sets that contain a spectrum id
    
    Parameters:
    
    spectrum_id, - the desired spectrum id
    
    Throws:
    
    SPECCHIOClientException
  - getUncertaintySetSpectraLists
```
java.util.ArrayList<UncertaintySetSpectraList> getUncertaintySetSpectraLists(java.util.ArrayList<java.lang.Integer> spectrum_ids)
                                                                      throws SPECCHIOClientException
```
    Retrieve uncertainty set ids where spectrum ids can be found
    
    Parameters:
    
    spectrum_ids -
    
    Returns:
    
    an arraylist of UncertaintySetSpectraList
    
    Throws:
    
    SPECCHIOClientException
  - getUncertaintySpaces
```
Space[] getUncertaintySpaces(java.util.ArrayList<java.lang.Integer> spectrum_ids,
                             java.util.ArrayList<java.lang.Integer> uncertainty_set_ids,
                             java.lang.String order_by)
                      throws SPECCHIOClientException
```
    Get the uncertainty spaces for a set of spectra and uncertainty set ids.
    
    Parameters:
    
    spectrum_ids - the spectrum identifiers
    
    uncertainty_set_ids - uncertainty set ids
    
    order_by - the field to order by
    
    Returns:
    
    an array of Space objects
    
    Throws:
    
    SPECCHIOClientException
  - getUsers
```
User[] getUsers()
         throws SPECCHIOClientException
```
    Get a list of all of the users in the database.
    
    Returns:
    
    an array of User objects
    
    Throws:
    
    SPECCHIOClientException
  - getUsersWithStatistics
```
User[] getUsersWithStatistics()
                       throws SPECCHIOWebClientException
```
    Get a list of all of the users in the database with added user statistics (number of loaded spectra, number of campaigns).
    
    Returns:
    
    an array of User objects
    
    Throws:
    
    SPECCHIOClientException
    
    SPECCHIOWebClientException
  - importCampaign
```
void importCampaign(int user_id,
                    java.io.InputStream is)
             throws SPECCHIOClientException
```
    Import a campaign.
    
    Parameters:
    
    user_id - the identifier of the user to whom the campaign will belong
    
    is - the input stream from which to read the campaign
    
    Throws:
    
    SPECCHIOClientException
  - importCampaign
```
void importCampaign(int user_id,
                    java.lang.String server_filepath)
             throws SPECCHIOWebClientException
```
    Import a campaign from a file that is on the Glassfish server (used for bigger files to prevent timeouts)
    
    Parameters:
    
    user_id - the identifier of the user to whom the campaign will belong
    
    server_filepath - the server filepath from which to read the campaign
    
    Throws:
    
    SPECCHIOWebClientException
  - insertCampaign
```
int insertCampaign(Campaign campaign)
            throws SPECCHIOClientException
```
    Insert a new campaign into the database
    
    Parameters:
    
    campaign - the campaign
    
    Returns:
    
    the identifier of the new campaign
    
    Throws:
    
    SPECCHIOClientException
  - insertHierarchy
```
int insertHierarchy(Campaign campaign,
                    java.lang.String name,
                    int parent_id)
             throws SPECCHIOClientException
```
    Insert a hierarchy node.
    
    Parameters:
    
    campaign - the campaign into which to insert the hierarchy
    
    name - the name of the new hierarchy
    
    parent_id - the identifier of the parent of the new hierarchy
    
    Returns:
    
    the identifier of the new hierarchy node
    
    Throws:
    
    SPECCHIOClientException
  - insertInstitute
```
int insertInstitute(Institute institute)
             throws SPECCHIOClientException
```
    Insert a new institute into the database
    
    Parameters:
    
    institute - an Instite object describing the new institute
    
    Returns:
    
    the identifier of the new institute
    
    Throws:
    
    SPECCHIOClientException
  - insertInstrumentCalibration
```
void insertInstrumentCalibration(Calibration c)
                          throws SPECCHIOClientException
```
    Insert calibration for an instrument.
    
    Parameters:
    
    c - the calibration data
    
    Throws:
    
    SPECCHIOClientException
  - insertInstrumentPicture
```
void insertInstrumentPicture(Picture picture)
                      throws SPECCHIOClientException
```
    Insert a picture of an instrument into the database.
    
    Parameters:
    
    picture - the picture
    
    Throws:
    
    SPECCHIOClientException
  - insertReferenceCalibration
```
void insertReferenceCalibration(Calibration c)
                         throws SPECCHIOClientException
```
    Insert calibration for a reference into the database.
    
    Parameters:
    
    c - the calibration data
    
    Throws:
    
    SPECCHIOClientException
  - insertReferencePicture
```
void insertReferencePicture(Picture picture)
                     throws SPECCHIOClientException
```
    Insert a picture associated with a reference into the database.
    
    Parameters:
    
    picture - the picture
    
    Throws:
    
    SPECCHIOClientException
  - insertSpectralFile
```
SpectralFileInsertResult insertSpectralFile(SpectralFile spec_file)
                                     throws SPECCHIOClientException
```
    Insert a spectral file into the database.
    
    Parameters:
    
    spec_file - the file
    
    Returns:
    
    a list of spectrum identifiers that were inserted into the database
    
    Throws:
    
    SPECCHIOClientException
  - insertClosestTargetReferenceLink
```
int insertClosestTargetReferenceLink(int target_id,
                                     java.util.ArrayList<java.lang.Integer> reference_ids)
                              throws SPECCHIOClientException
```
    Insert a target-reference link to closest reference on acquisition timeline
    
    Parameters:
    
    target_id - the identifier of the target node
    
    reference_ids - the identifiers of the reference nodes
    
    Returns:
    
    the number of links sucessfully created
    
    Throws:
    
    SPECCHIOClientException
  - insertSpectrumSubset
```
int insertSpectrumSubset(UncertaintySpectrumNode uc_spectrum_node)
                  throws SPECCHIOClientException
```
    Insert a spectrum subset
    
    Parameters:
    
    spectrum - node a spectrum node
    
    Returns:
    
    the id of the created spectrum subset
    
    Throws:
    
    SPECCHIOClientException
  - insertUncertaintyNode
```
int insertUncertaintyNode(UncertaintySpectrumNode uc_spectrum_node,
                          int uc_set_id)
                   throws SPECCHIOClientException
```
    Insert an uncertainty node
    
    Parameters:
    
    uc_spectrum_node - an uncertainty node of type spectrum
    
    Returns:
    
    the id of the created node
    
    Throws:
    
    SPECCHIOClientException
  - insertUncertaintyNode
```
int insertUncertaintyNode(UncertaintyInstrumentNode uc_instrument_node,
                          int uc_set_id)
                   throws SPECCHIOClientException
```
    Insert an uncertainty node
    
    Parameters:
    
    uc_instrument_node - an uncertainty node of type instrument
    
    Returns:
    
    the id of the created node
    
    Throws:
    
    SPECCHIOClientException
  - insertNewUncertaintySet
```
int insertNewUncertaintySet(UncertaintySet uc_set)
                     throws SPECCHIOClientException
```
    Insert new uncertainty set
    
    Parameters:
    
    uc_set -
    
    Returns:
    
    the id of the created set
    
    Throws:
    
    SPECCHIOClientException
  - getAdjacencyMatrix
```
AdjacencyMatrix getAdjacencyMatrix(int uncertainty_set_id)
                            throws SPECCHIOClientException
```
    Get the adjacency matrix for a given uncertainty set
    
    Parameters:
    
    uncertainty_set_id - the uncertainty set identifier
    
    Returns:
    
    an array of integers of the adjacency matrix
    
    Throws:
    
    SPECCHIOClientException
  - getEdgeValue
```
java.lang.String getEdgeValue(int edge_id)
                       throws SPECCHIOClientException
```
    Get an edge value for a given edge id
    
    Parameters:
    
    edge_id -
    
    Returns:
    
    an edge value
    
    Throws:
    
    SPECCHIOClientException
  - getUncertaintyInstrumentNode
```
UncertaintyNode getUncertaintyInstrumentNode(int instrument_node_id)
                                      throws SPECCHIOClientException
```
    Get instrument node for a selected instrument id
    
    Parameters:
    
    instrument_node_id - instrument node id
    
    Returns:
    
    an InstrumentNode
    
    Throws:
    
    SPECCHIOClientException
  - insertUncertaintyInstrumentNode
```
int insertUncertaintyInstrumentNode(UncertaintyInstrumentNode instrument_node)
                             throws SPECCHIOClientException
```
    Insert an instrument node into the database.
    
    Parameters:
    
    instrument_node - UncertaintyInstrumentNode type
    
    Returns:
    
    an instrument_node_id
    
    Throws:
    
    SPECCHIOClientException
  - getUncertaintyNodeComponents
```
UncertaintyNode[] getUncertaintyNodeComponents(int uncertainty_node_id)
                                        throws SPECCHIOClientException
```
    Retrieve an uncertainty node.
    
    Parameters:
    
    uncertainty_node_id -
    
    Returns:
    
    the corresponding uncertainty node
    
    Throws:
    
    SPECCHIOClientException
  - getUncertaintyNodeSubSets
```
UncertaintyNode[] getUncertaintyNodeSubSets(int uncertainty_node_id)
                                     throws SPECCHIOClientException
```
    Retrieve uncertainty node subsets.
    
    Parameters:
    
    uncertainty_node_id -
    
    Returns:
    
    the corresponding uncertainty node components grouped into subsets that make up this combined node
    
    Throws:
    
    SPECCHIOClientException
  - getUncertaintySpectrumNode
```
UncertaintyNode getUncertaintySpectrumNode(int spectrum_node_id)
                                    throws SPECCHIOClientException
```
    Get spectrum node for a selected spectrum node id
    
    Parameters:
    
    spectrum_node_id - spectrum node id
    
    Returns:
    
    an InstrumentNode
    
    Throws:
    
    SPECCHIOClientException
  - insertTargetReferenceLinks
```
int insertTargetReferenceLinks(int target_id,
                               java.util.ArrayList<java.lang.Integer> reference_ids)
                        throws SPECCHIOClientException
```
    Insert a target-reference links.
    
    Parameters:
    
    target_id - the identifier of the target node
    
    reference_ids - the identifiers of the reference nodes
    
    Returns:
    
    the number of links sucessfully created
    
    Throws:
    
    SPECCHIOClientException
  - instrumentCalibrationExists
```
boolean instrumentCalibrationExists(Calibration cal)
                             throws SPECCHIOWebClientException
```
    Test for the existence of a calibration in the database.
    
    Parameters:
    
    cal - calibration object to check
    
    Returns:
    
    true if the calibration already exists in the database, false otherwise
    
    Throws:
    
    SPECCHIOWebClientException
  - isLoggedInWithRole
```
boolean isLoggedInWithRole(java.lang.String roleName)
                    throws SPECCHIOClientException
```
    Test whether or not the client is logged in under a given role.
    
    Parameters:
    
    roleName - the role to be tested
    
    Returns:
    
    "true" if the client is logged in as a user with role roleIn, "false" otherwise
    
    Throws:
    
    SPECCHIOClientException
  - loadMetaparameter
```
MetaParameter loadMetaparameter(int metaparameter_id)
                         throws SPECCHIOClientException
```
    Get the meta-parameter of the given metaparameter identifier.
    
    Parameters:
    
    metaparameter_id - the metaparameter identifier for which to retrieve metadata
    
    Returns:
    
    the meta-parameter object corresponding to the desired id
    
    Throws:
    
    SPECCHIOClientException
  - loadSensor
```
void loadSensor(java.io.InputStream is)
         throws SPECCHIOClientException
```
    Load a sensor definition into the database from an input stream.
    
    Parameters:
    
    is - the input stream
    
    Throws:
    
    SPECCHIOClientException
  - loadSpace
```
Space loadSpace(Space space)
         throws SPECCHIOClientException
```
    Load a Space object.
    
    Parameters:
    
    space - a partially-filled space object
    
    Returns:
    
    a complete Space object
    
    Throws:
    
    SPECCHIOClientException
  - moveHierarchy
```
boolean moveHierarchy(int source_hierarchy_id,
                      int target_parent_hierarchy)
               throws SPECCHIOClientException
```
    Move a hierarchy to a new parent hierarchy within the same campaign. If a hierarchy of the same name exists in the target hierarchy then the hierarchies are merged.
    
    Parameters:
    
    source_hierarchy_id - hierarchy id of the hierarchy to move
    
    target_parent_hierarchy - hierarchy id of the new parent hierarchy return true if move was done
    
    Throws:
    
    SPECCHIOClientException
  - refreshMetadataCategory
```
void refreshMetadataCategory(java.lang.String field)
```
    Causes the client to reload data values the specified category upon next request.
    
    Parameters:
    
    field - name
  - removeEavMetadata
```
void removeEavMetadata(MetaParameter mp)
                throws SPECCHIOClientException
```
    Remove an item of EAV metadata.
    
    Parameters:
    
    mp - the meta-parameter to be removed
    
    Throws:
    
    SPECCHIOClientException
  - removeEavMetadata
```
void removeEavMetadata(MetaParameter mp,
                       java.util.ArrayList<java.lang.Integer> spectrum_ids)
                throws SPECCHIOClientException
```
    Remove an item of EAV metadata for a collection of spectra.
    
    Parameters:
    
    mp - the meta-parameter to be removed
    
    spectrum_ids - the spectrum identifiers
    
    Throws:
    
    SPECCHIOClientException
  - removeEavMetadata
```
void removeEavMetadata(attribute attr,
                       java.util.ArrayList<java.lang.Integer> spectrum_ids,
                       int metadata_level)
                throws SPECCHIOClientException
```
    Remove one or more items of EAV metadata for a collection of spectra for a defined attribute.
    
    Parameters:
    
    attr - the attribute to be removed
    
    spectrum_ids - the spectrum identifiers
    
    metadata_level - storage level identifier
    
    Throws:
    
    SPECCHIOClientException
  - removeSpectralNode
```
void removeSpectralNode(spectral_node_object sn)
                 throws SPECCHIOClientException
```
    Remove the data corresponding to a node of the spectral data browser.
    
    Parameters:
    
    sn - the node to be removed
    
    Throws:
    
    SPECCHIOClientException
  - removeSpectralNodes
```
void removeSpectralNodes(java.util.ArrayList<spectral_node_object> sns)
                  throws SPECCHIOWebClientException
```
    Remove the data corresponding to a node of the spectral data browser.
    
    Parameters:
    
    sns - list of nodes to be removed
    
    Throws:
    
    SPECCHIOWebClientException
  - renameHierarchy
```
boolean renameHierarchy(int hierarchy_id,
                        java.lang.String name)
                 throws SPECCHIOClientException
```
    Rename a hierarchy in the database and also on the file system if path is accessible. The rename on the database will only be applied if a rename on the file system succeeded.
    
    Parameters:
    
    hierarchy_id - id of the hierarchy to be renamed
    
    name - new name of the hierarchy
    
    Returns:
    
    true if and only if the renaming succeeded; false otherwise
    
    Throws:
    
    SPECCHIOClientException
  - setProgressReport
```
void setProgressReport(ProgressReportInterface pr)
```
    Set the progress report interface to which progress made by this client will be reported.
    
    Parameters:
    
    pr - the progress report; use null to report no progress
  - sortByAttributes
```
AVMatchingListCollection sortByAttributes(java.util.ArrayList<java.lang.Integer> spectrum_ids,
                                          java.lang.String... attribute_names)
                                   throws SPECCHIOClientException
```
    Sort spectra by the values of the specified attributes
    
    Parameters:
    
    spectrum_ids - list of ids to sort
    
    attribute_names - attribute names to sort by
    
    Returns:
    
    a AVMatchingListCollection object
    
    Throws:
    
    SPECCHIOClientException
  - spectralFileExists
```
boolean spectralFileExists(SpectralFile spec_file)
                    throws SPECCHIOClientException
```
    Test for the existence of a spectral file in the database.
    
    Parameters:
    
    spec_file - spectral file object to check
    
    Returns:
    
    true if the file already exists in the database, false otherwise
    
    Throws:
    
    SPECCHIOClientException
  - spectralFilesExist
```
boolean[] spectralFilesExist(SpectralFiles spec_files)
                      throws SPECCHIOClientException
```
    Test for the existence of a spectral files in the database.
    
    Parameters:
    
    spec_files - container with arraylist of spectral files to check
    
    Returns:
    
    array of boolean values indicating existence
    
    Throws:
    
    SPECCHIOClientException
  - submitRDACollection
```
java.lang.String submitRDACollection(RDACollectionDescriptor collection_d)
                              throws SPECCHIOClientException
```
    Submit a collection to Research Data Australia.
    
    Parameters:
    
    collection_d - the collection descriptor
    
    Returns:
    
    the collection identifier of the new collection, or an empty string if publication failed
    
    Throws:
    
    SPECCHIOClientException - could not contact the server
  - updateCampaign
```
void updateCampaign(Campaign campaign)
             throws SPECCHIOClientException
```
    Update the information about a campaign
    
    Parameters:
    
    campaign - the new campaign data
    
    Throws:
    
    SPECCHIOClientException
  - updateEavMetadata
```
int updateEavMetadata(MetaParameter mp,
                      java.util.ArrayList<java.lang.Integer> spectrum_ids)
               throws SPECCHIOClientException
```
    Update EAV metadata.
    
    Parameters:
    
    mp - the meta-parameter to update
    
    spectrum_ids - the identifiers for which to update the parameter
    
    Returns:
    
    the identifier of the inserted metadata
    
    Throws:
    
    SPECCHIOClientException
  - updateEavMetadata
```
int updateEavMetadata(MetaParameter mp,
                      java.util.ArrayList<java.lang.Integer> spectrum_ids,
                      MetaParameter mp_old)
               throws SPECCHIOClientException
```
    Update EAV metadata.
    
    Parameters:
    
    mp - the meta-parameter to update
    
    spectrum_ids - the identifiers for which to update the parameter
    
    mp_old - the old meta-parameter
    
    Returns:
    
    the identifier of the inserted metadata
    
    Throws:
    
    SPECCHIOClientException
  - updateEavMetadataAnnotation
```
int updateEavMetadataAnnotation(MetaParameter mp,
                                java.util.ArrayList<java.lang.Integer> spectrum_ids)
                         throws SPECCHIOWebClientException
```
    Update EAV metadata annotation.
    
    Parameters:
    
    mp - the meta-parameter to update
    
    spectrum_ids - the identifiers for which to update the parameter
    
    Returns:
    
    the identifier of the inserted metadata
    
    Throws:
    
    SPECCHIOWebClientException
  - updateOrInsertEavMetadata
```
int updateOrInsertEavMetadata(MetaParameter mp,
                              java.util.ArrayList<java.lang.Integer> spectrum_ids)
                       throws SPECCHIOWebClientException
```
    Update or insert EAV metadata. Will automatically update existing entries or insert a new metaparameter if not existing.
    
    Parameters:
    
    mp - the meta-parameter to update or insert
    
    spectrum_ids - the identifiers for which to update or insert the parameter
    
    Returns:
    
    the identifier of the inserted or updated metadata
    
    Throws:
    
    SPECCHIOWebClientException
  - updateOrInsertEavMetadata
```
int updateOrInsertEavMetadata(MetaParameter mp,
                              int spectrum_id)
                       throws SPECCHIOWebClientException
```
    Update or insert EAV metadata. Will automatically update existing entries or insert a new metaparameter if not existing.
    
    Parameters:
    
    mp - the meta-parameter to update or insert
    
    spectrum_id - the identifiers for which to update or insert the parameter
    
    Returns:
    
    the identifier of the inserted or updated metadata
    
    Throws:
    
    SPECCHIOWebClientException
  - updateOrInsertEavMetadata
```
int updateOrInsertEavMetadata(java.util.ArrayList<Metadata> md,
                              java.util.ArrayList<java.lang.Integer> ids,
                              int campaignId)
                       throws SPECCHIOWebClientException
```
    Update or insert EAV metadata. Will automatically update existing entries or insert a new metaparameter if not existing.
    
    Parameters:
    
    md - list containing all metadata
    
    Returns:
    
    the identifier of the inserted or updated metadata
    
    Throws:
    
    SPECCHIOWebClientException
  - updateInstrument
```
void updateInstrument(Instrument instrument)
               throws SPECCHIOClientException
```
    Update an instrument.
    
    Parameters:
    
    instrument - the instrument
    
    Throws:
    
    SPECCHIOClientException
  - updateInstrumentCalibrationMetadata
```
void updateInstrumentCalibrationMetadata(CalibrationMetadata cm)
                                  throws SPECCHIOClientException
```
    Update the calibration metadata for an instrument.
    
    Parameters:
    
    cm - the calibration metadata
    
    Throws:
    
    SPECCHIOClientException
  - updateInstrumentPicture
```
void updateInstrumentPicture(Picture picture)
                      throws SPECCHIOClientException
```
    Update a picture associated with an instrument.
    
    Parameters:
    
    picture - the picture
    
    Throws:
    
    SPECCHIOClientException
  - updateReference
```
void updateReference(Reference reference)
              throws SPECCHIOClientException
```
    Update an reference.
    
    Parameters:
    
    reference - the reference
    
    Throws:
    
    SPECCHIOClientException
  - updateReferenceCalibrationMetadata
```
void updateReferenceCalibrationMetadata(CalibrationMetadata cm)
                                 throws SPECCHIOClientException
```
    Update the calibration metadata for a reference.
    
    Parameters:
    
    cm - the calibration metadata
    
    Throws:
    
    SPECCHIOClientException
  - updateReferencePicture
```
void updateReferencePicture(Picture picture)
                     throws SPECCHIOClientException
```
    Update a picture associated with a reference.
    
    Parameters:
    
    picture - the picture
    
    Throws:
    
    SPECCHIOClientException
  - updateSpectraMetadata
```
void updateSpectraMetadata(java.util.ArrayList<java.lang.Integer> ids,
                           java.lang.String field,
                           int id)
                    throws SPECCHIOClientException
```
    Update the metadata fields for a set of spectra
    
    Parameters:
    
    ids - the spectrum identifiers
    
    field - the name of the field to be updated
    
    id -
    
    Throws:
    
    SPECCHIOClientException
  - updateSpectrumVector
```
void updateSpectrumVector(int spectrum_id,
                          float[] vector)
                   throws SPECCHIOClientException
```
    Update the spectral vector of a spectrum
    
    Parameters:
    
    spectrum_id - the spectrum identifier
    
    vector - new spectral data
    
    Throws:
    
    SPECCHIOClientException
  - updateSpectrumVectors
```
void updateSpectrumVectors(java.util.HashMap<java.lang.Integer,double[]> updateMap)
                    throws SPECCHIOClientException
```
    Update the spectral vector of a spectrum
    
    Parameters:
    
    updateMap - a map containing the spectrum_id as key and the vector as value
    
    Throws:
    
    SPECCHIOClientException
  - updateUser
```
void updateUser(User user)
         throws SPECCHIOClientException
```
    Update the information about a user.
    
    Parameters:
    
    user - the user data
    
    Throws:
    
    SPECCHIOClientException

Interface SPECCHIOClient

Method Summary

Method Detail

connect

close

copySpectrum

copySpectra

copyHierarchy

clearMetaparameterRedundancyList

createUserAccount

createUserAccountOnCurrentServer

createInstrument

createReference

dbUpgrade

deleteCalibration

deleteInstrument

deleteInstrumentPicture

deleteReference

deleteReferencePicture

deleteTargetReferenceLinks

disconnect

filterSpectrumIdsByHavingAttribute

filterSpectrumIdsByNotHavingAttribute

filterSpectrumIdsByHavingAttributeValue

getMetadataCategoriesForApplicationDomains

getAttributesForCategory

getAttributes

getAttributesIdHash

getAttributesNameHash

getAttributeUnits

getCampaign

getCategoriesInfo

getNonNullCategories

getNonNullAttributes

findMatchingSpectra

createFilterCollection

getCampaignExportInputStream

getCampaignNode

getCampaigns

getCampaigns

getCalibrationIds

getCalibratedInstrument

getCalibrationMetadataByCalibrationNumber

getCapability

getChildrenOfNode

getChildrenOfTaxonomyNode

getCountries

getDatabaseNode

getDirectHierarchyId

getDirectHierarchyIds

getDistinctValuesOfAttribute

getEavMetadataConflicts

getEAVQueryConditionObject

getExistingMetaparameterCount

getFileFormatId

getHierarchy

getHierarchyId

getHierarchyIdsOfSpectra

getHierarchyParentId

getHierarchyFilePath

getHierarchyName

getInstitutes

getInstrument

getInstrument

getInstrumentIds

getInstrumentCalibrationMetadata

getInstrumentDescriptors

getInstrumentForSpectralFile

getInstrumentPictures

getLoggedInUser

getMetadataCategoriesForApplicationDomain

getMetadataCategoriesForIdAccess

getMetadataCategoriesForNameAccess

getMetaparameters

calculateSunAngle

getMetaparameter

getMetaparameters

getMetaparameters

getMetaparameterStatistics

getMetaparameterValues