Class OpenBISScreeningML


  • public class OpenBISScreeningML
    extends java.lang.Object
    Simple Matlab interface for openBIS for Screening. It is meant to be used in one Matlab session at a time, i.e. it is not multi-threading safe.

    While written in Java, the API is idiomatic for Matlab, i.e. values are returned as multi-dimensional arrays. For the get... and load... methods the first index will contain the actual data, while the second index will contain per-row annotations. For getFeatureMatrix, the third index contains per-column annotations. This allows simple access with Matlab's slicing operator, see doc of e.g. getFeatureMatrix(String, String, String[]).

    A typical Matlab session looks like:

     % Add the API jar file to the classpath
     javaaddpath('/home/brinn/matlab/openbis_screening_api-batteries_included.jar')
     % Login to server
     OpenBISScreeningML.login('user', 'secret', 'https://www.infectome.org')
     
     % ...perform calls on the server...
     
     % Logout to close the session on the server
     OpenBISScreeningML.logout()
     
    Note: using this login your password will end up in the Matlab command history. An alternative that avoids this is to call the Login class. Logging in on the console will grant this class access to the openBIS server.

    To learn the API one needs to understand three basic notions: code, augmented code and perm id. Space, project, experiment, plate and well have their own code, which is unique only in the context of the parent.
    That's why one needs augmented code to point e.g. to one experiment, because two different projects can have experiments with the same code.
    Such an augmented code for experiment has a form of "/space-code/project-code/experiment-code".
    For plate it has a form of "/space-code/plate-code" (note that plate code is unique on the space level).
    The drawback of an augmented code is that it's not persistent. If someone e.g. moves the experiment from one space to the other augmented code of the experiment becomes invalid. That is why experiments, plates and datasets have perm id (permament identifier) which never change and allow to refer to them with one "magic" identifier, e.g. 20110516124520378-737166.

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static java.lang.String REQUIRES_OPENBIS_AS_API
      The required version ("major.minor") of the screening API on the openBIS application server.
      static java.lang.String REQUIRES_OPENBIS_DSS_API
      The required version ("major.minor") of the screening API on the openBIS datastore server.
      static java.lang.String VERSION
      The version of the API.
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static java.lang.String getContainerDataSetCode​(java.lang.String dataSetCode)  
      static java.lang.Object[][][] getDataSetMetaData​(java.lang.String[] dataSetCodes)
      Lists meta data of specified data sets.
      static java.lang.Object[][][][] getFeatureMatrix​(java.lang.String gene, java.lang.String analysisProcedureOrNull, java.lang.String[] featuresOrNull)
      Returns the feature matrix of the specified features for all locations (a location is one well position in one feature vector data set) in experiment connected to gene in [0], location annotations in [1] and feature annotation in [2].
      static java.lang.Object[][][][] getFeatureMatrix​(java.lang.String experiment, java.lang.String gene, java.lang.String analysisProcedureOrNull, java.lang.String[] featuresOrNull)
      Returns the feature matrix of the specified features for all locations in experiment (a location is one well position in one feature vector data set) in experiment connected to gene in [0], location annotations in [1] and feature annotation in [2].
      static java.lang.Object[][][][] getFeatureMatrixForPlate​(java.lang.String plate, java.lang.String analysisProcedureOrNull, java.lang.String[] featuresOrNull)
      Returns the feature matrix of the specified features for all locations (a location is one well position in one feature vector data set) of all feature vector data sets created by specified analysis procedure of the given plate in [0], location annotations in [1] and feature annotation in [2].
      static java.lang.Object[][][] getGeneMappingForPlates​(java.lang.String[] platesCodes)
      Returns the gene mapping for the given plateCodes in [0] and location annotations in [1].
      static java.lang.Object[][] getImagesMetadata​(java.lang.String augmentedPlateCode)
      Fetches metadata of the image datasets for the specified plate.
      protected static java.io.File getLinkOrCopyOfContents​(java.lang.String overrideStoreRootPathOrNull, DataSet dataSet, java.io.File file)  
      static PlateMetadata[] getPlateMetadataList​(java.lang.String[] platesCodes)
      Experimental method that returns an array of PlateMetadata Java objects for a given list of plate codes.
      static java.lang.Object[][] getPlateProperties​(java.lang.String augmentedPlateCode)
      Returns the properties of specified plate.
      static java.lang.Object[][] getWellProperties​(java.lang.String augmentedPlateCode, int row, int column)
      Returns the properties of specified well for specified plate.
      static java.lang.Object[][] listAnalysisProcedures​(java.lang.String experiment)
      Returns an alphabetically sorted list of analysis procedure codes of all data sets of a specified experiment.
      static java.lang.Object[][] listChannels​(java.lang.String experiment)
      Lists all channels measured in experiment.
      static java.lang.Object[][][] listDataSetFilesForExperiment​(java.lang.String augmentedExperimentCode, java.lang.String dataSetTypeCodePattern)
      Lists all files of all data sets for specified experiment and data set type code matching specified regular expression pattern.
      static java.lang.Object[][][] listDataSetsFiles​(java.lang.String augmentedPlateCode, java.lang.String dataSetTypeCodePattern)
      Lists all files of all data sets for specifies plate and data set type code matching specified regular expression pattern.
      static java.lang.Object[][] listExperiments()
      Lists all experiment.
      static java.lang.Object[][] listFeatures​(java.lang.String experiment, java.lang.String analysisProcedureOrNull)
      Lists all features computed for experiment using specified analysis procedure.
      static java.lang.Object[][][] listMaterials​(java.lang.String materialType)
      List all material of a given type.
      static java.lang.Object[][] listPlates()
      Lists all plates.
      static java.lang.Object[][] listPlates​(java.lang.String experiment)
      Lists the plates of experiment.
      static java.lang.Object[][] listPlates​(java.lang.String experiment, java.lang.String analysisProcedure)
      Lists the plates of experiment and analysis procedure.
      static java.lang.Object[][] listSegmentationObjects​(java.lang.String plate, java.lang.String analysisProcedureOrNull)
      Lists all segmentation objects for the plate.
      static java.lang.Object loadDataSetFile​(java.lang.String dataSetCode, java.lang.String pathInDataSet, java.lang.String overrideStoreRootPathOrNull)
      Loads file/folder of specified data set and specified file/folder path inside the data set.
      static java.lang.Object[][] loadDataSets​(java.lang.String augmentedPlateCode, java.lang.String dataSetTypeCodePattern, java.lang.Object[][] properties, java.lang.String overrideStoreRootPathOrNull)
      Loads data sets for specified plate code.
      static java.lang.Object[][] loadDataSets​(java.lang.String augmentedPlateCode, java.lang.String dataSetTypeCodePattern, java.lang.String overrideStoreRootPathOrNull)
      Loads data sets for specified plate code.
      static java.lang.Object[][] loadDataSetsForExperiment​(java.lang.String augmentedExperimentCode, java.lang.String dataSetTypeCodePattern, java.lang.Object[][] properties, java.lang.String overrideStoreRootPathOrNull)
      Loads data sets for specified experiment code.
      static java.lang.Object[][][] loadImages​(java.lang.String plate, int row, int col)
      Loads the TIFF images for the given well location, all tiles and all channels and stores them in temporary files.
      static java.lang.Object[][][] loadImages​(java.lang.String plate, int row, int col, int tile)
      Loads the TIFF images for the given well location, tile number, and all channels and stores them in temporary files.
      static java.lang.Object[][][] loadImages​(java.lang.String plate, int row, int col, int tile, java.lang.String[] channels)
      Loads the TIFF images for the given well location, tile number, and list of channels and stores them in temporary files.
      static java.lang.Object[][][] loadImages​(java.lang.String plate, int row, int col, java.lang.String[] channels)
      Loads the TIFF images for the given well location, list of channels, and all tiles and stores them in temporary files.
      static java.lang.Object[][][] loadSegmentationImages​(java.lang.String plate, int row, int col, int tile, java.lang.String[] objectNamesOrNull, java.lang.String analysisProcedureOrNull)
      Has the same effect as loadImages(String, int, int, int, String[]), but instead of loading raw images loads their segmentation results if available.
      static java.lang.Object[][][] loadSegmentationImages​(java.lang.String plate, int row, int col, java.lang.String[] objectNamesOrNull, java.lang.String analysisProcedureOrNull)
      Has the same effect as loadImages(String, int, int, String[]), but instead of loading raw images loads their segmentation results if available.
      static void login​(java.lang.String user, java.lang.String password, java.lang.String url)
      Login to the openBIS server given as url.
      static void logout()
      Logs out and closes the session on the server.
      static void updatePlateProperties​(java.lang.String augmentedPlateCode, java.lang.Object[][] properties)
      Updates properties of specified plate.
      static void updateWellProperties​(java.lang.String augmentedPlateCode, int row, int column, java.lang.Object[][] properties)
      Updates properties of specified well for specified plate.
      static java.lang.Object uploadDataSet​(java.lang.String augmentedPlateCode, java.lang.String dataSetFilePath, java.lang.String dataSetType, java.lang.Object[][] dataSetProperties)
      Uploads specified data set for specified plate.
      static java.lang.Object uploadDataSetForExperimentAndParents​(java.lang.String augmentedExperimentCode, java.lang.Object[] parentDataSetCodeObjects, java.lang.String dataSetFilePath, java.lang.String dataSetType, java.lang.Object[][] dataSetProperties)
      Uploads a data set to the specified experiment, setting the data set parents.
      static java.lang.Object uploadDataSetForPlateAndParents​(java.lang.String augmentedPlateCode, java.lang.Object[] parentDataSetCodeObjects, java.lang.String dataSetFilePath, java.lang.String dataSetType, java.lang.Object[][] dataSetProperties)
      Uploads specified data set for specified plate.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Field Detail

      • VERSION

        public static final java.lang.String VERSION
        The version of the API.
        See Also:
        Constant Field Values
      • REQUIRES_OPENBIS_AS_API

        public static final java.lang.String REQUIRES_OPENBIS_AS_API
        The required version ("major.minor") of the screening API on the openBIS application server.
        See Also:
        Constant Field Values
      • REQUIRES_OPENBIS_DSS_API

        public static final java.lang.String REQUIRES_OPENBIS_DSS_API
        The required version ("major.minor") of the screening API on the openBIS datastore server.
        See Also:
        Constant Field Values
    • Method Detail

      • login

        public static void login​(java.lang.String user,
                                 java.lang.String password,
                                 java.lang.String url)
        Login to the openBIS server given as url.

        Matlab example:

         OpenBISScreeningML.login('user', 'secret', 'https://www.infectome.org')
         
        Parameters:
        user - The user id on the server
        password - The password on the server
        url - The URL, e.g. https://www.infectome.org
      • logout

        public static void logout()
        Logs out and closes the session on the server.

        Matlab example:

         OpenBISScreeningML.logout()
         
      • listExperiments

        public static java.lang.Object[][] listExperiments()
        Lists all experiment.

        Matlab example:

         % Get the experiments
         exps = OpenBISScreeningML.listExperiments();
         % How many experiments do we have?
         length(exps)
         % Get all information about experiment 3
         exp3 = exps(3,:)
         % Get the perm ids for all experiments
         permids = exps(:,2)
         
        Returns:
        Each row contains information about one experiment:

        { experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code }

      • listPlates

        public static java.lang.Object[][] listPlates()
        Lists all plates.

        Matlab example:

         % Get the plates
         plates = OpenBISScreeningML.listPlates();
         % How many plates do we have?
         length(plates)
         % Get all information about plate 2
         plate2 = plates(2,:)
         % Get the simple plate codes for all plates
         codes = plates(:,4)
         
        Returns:
        Each row contains information about one plate:

        { plate augmented code, plate perm id, plate space code, plate code, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code }

      • listPlates

        public static java.lang.Object[][] listPlates​(java.lang.String experiment)
        Lists the plates of experiment.

        Matlab example:

         % Get the plates of experiment MYEXP in project PROJ of space SPACE
         plates = OpenBISScreeningML.listPlates('/SPACE/PROJ/MYEXP');
         % How many plates do we have?
         length(plates)
         % Get all information about plate 2
         plate2 = plates(2,:)
         % Get the augmented plate codes for all plates
         acodes = plates(:,1)
         
        Parameters:
        experiment - The augmented code of the experiment to list the plates for
        Returns:
        Each row contains information about one plate:

        { plate augmented code, plate perm id, plate space code, plate code, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code }

      • listPlates

        public static java.lang.Object[][] listPlates​(java.lang.String experiment,
                                                      java.lang.String analysisProcedure)
        Lists the plates of experiment and analysis procedure. Each returned plate has at least one data set with the specified analysis procedure.

        Matlab example:

         % Get all plates having data sets with analysis procedure 'PROC' in the experiment MYEXP in project PROJ of space SPACE
         plates = OpenBISScreeningML.listPlates('/SPACE/PROJ/MYEXP', 'PROC');
         % Get all information about plate 2
         plate2 = plates(2,:)
         % Get the augmented plate codes for all plates
         acodes = plates(:,1)
         
        Parameters:
        experiment - The augmented code of the experiment to list the plates for
        analysisProcedure - The analysis procedure
        Returns:
        Each row contains information about one plate:

        { plate augmented code, plate perm id, plate space code, plate code, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code }

      • listAnalysisProcedures

        public static java.lang.Object[][] listAnalysisProcedures​(java.lang.String experiment)
        Returns an alphabetically sorted list of analysis procedure codes of all data sets of a specified experiment.

        Matlab example:

         % Get the analysis procedures for experiment MYEXP in project PROJ of space SPACE
         analysisProcedures = OpenBISScreeningML.listAnalysisProcedures('/SPACE/PROJ/MYEXP');
         % How many analysis procedures do we have?
         length(analysisProcedures)
         % Get all the analysis procedure codes 
         acodes = analysisProcedures(:,1)
         
        Parameters:
        experiment - The augmented code of the experiment to list analysis procedures for
        Returns:
        Each row contains information about one analysis procedure:

        { analysis procedure code }

      • listMaterials

        public static java.lang.Object[][][] listMaterials​(java.lang.String materialType)
        List all material of a given type.

        Matlab example:

         % List all SIRNA material
         sirna = OpenBISScreeningML.listMaterials('SIRNA')
         % All material codes
         sirna(:,1,1)
         % All material ids
         sirna(:,2,1)
         % Properties of first material
         metadata(1,3,:)
         
        Parameters:
        materialType - Material type as string.
        Returns:
        For each data set: {{material code}, {material id}, { {key1, value1}, {key2, value2} ... } }
      • getPlateProperties

        public static java.lang.Object[][] getPlateProperties​(java.lang.String augmentedPlateCode)
        Returns the properties of specified plate.

        Matlab example:

         % Get properties for plate P005 in space SPACE
         properties = OpenBISScreeningML.getPlateProperties('/SPACE/P005')
         % Get property type code of first property
         properties(1,1)
         % Get property value of first property
         properties(1,2)
         
        Parameters:
        augmentedPlateCode - The augmented plate code
        Returns:
        A two dimensional array where the first column contains the property codes and the second column the corresponding property values.
      • updatePlateProperties

        public static void updatePlateProperties​(java.lang.String augmentedPlateCode,
                                                 java.lang.Object[][] properties)
        Updates properties of specified plate.

        Matlab example:

         % Updates properties DESCRIPTION and NUMBER for plate P005 in space SPACE
         properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
         OpenBISScreeningML.updatePlateProperties('/SPACE/P005', properties)
         
        Parameters:
        augmentedPlateCode - The augmented plate code
        properties - A two dimensional array where the first column contains the property codes and the second column the corresponding property values.
      • getWellProperties

        public static java.lang.Object[][] getWellProperties​(java.lang.String augmentedPlateCode,
                                                             int row,
                                                             int column)
        Returns the properties of specified well for specified plate.

        Matlab example:

         % Get properties for well A03 of plate P005 in space SPACE
         properties = OpenBISScreeningML.getWellProperties('/SPACE/P005', 1, 3)
         % Get property type code of first property
         properties(1,1)
         % Get property value of first property
         properties(1,2)
         
        Parameters:
        augmentedPlateCode - The augmented plate code
        row - The row in the plate to get the well properties for
        column - The column in the plate to get the well properties for
        Returns:
        A two dimensional array where the first column contains the property codes and the second column the corresponding property values.
      • updateWellProperties

        public static void updateWellProperties​(java.lang.String augmentedPlateCode,
                                                int row,
                                                int column,
                                                java.lang.Object[][] properties)
        Updates properties of specified well for specified plate.

        Matlab example:

         % Updates properties DESCRIPTION and NUMBER for well A03 of plate P005 in space SPACE
         properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
         OpenBISScreeningML.updateWellProperties('/SPACE/P005', 1, 3, properties)
         
        Parameters:
        augmentedPlateCode - The augmented plate code
        row - The row in the plate to get the well properties for
        column - The column in the plate to get the well properties for
        properties - A two dimensional array where the first column contains the property codes and the second column the corresponding property values.
      • getImagesMetadata

        public static java.lang.Object[][] getImagesMetadata​(java.lang.String augmentedPlateCode)
        Fetches metadata of the image datasets for the specified plate.

        Matlab example:

         % Get the metadata of image datasets of plate P005 from space SPACE
         imagesMetadata = OpenBISScreeningML.getImagesMetadata('/SPACE/P005');
         % How many image datasets do we have? Usually there will be just one.
         length(imagesMetadata)
         % What is the number of tiles in the first image dataset?
         imagesMetadata(1, 3)
         
        Parameters:
        augmentedPlateCode - The augmented plate code.
        Returns:
        { images width, images height, number of tiles in the well, number of tiles rows, number of tiles columns, number of plate rows, number of plate columns } .
      • listChannels

        public static java.lang.Object[][] listChannels​(java.lang.String experiment)
        Lists all channels measured in experiment.

        Matlab example:

         % Get the channels of experiment MYEXP in project PROJ of space SPACE
         channels = OpenBISScreeningML.listChannels('/SPACE/PROJ/MYEXP');
         % How many channels do we have?
         length(channels)
         % What is the name of channel 1?
         channels(1)
         
        Parameters:
        experiment - The augmented code of the experiment to list the channels for
        Returns:
        Each row contains information about one channel. Currently the only information available is the channel name.
      • listFeatures

        public static java.lang.Object[][] listFeatures​(java.lang.String experiment,
                                                        java.lang.String analysisProcedureOrNull)
        Lists all features computed for experiment using specified analysis procedure.

        Matlab example:

         % Get the features of experiment MYEXP in project PROJ of space SPACE
         features = OpenBISScreeningML.listFeatures('/SPACE/PROJ/MYEXP', []);
         % Get the features of experiment MYEXP in project PROJ of space SPACE which are computed
         % with analysis procedure AP-4711
         features = OpenBISScreeningML.listFeatures('/SPACE/PROJ/MYEXP', 'AP-4711');
         % How many features do we have?
         length(features)
         % What is the name of features 1?
         features(1)
         
        Parameters:
        experiment - The augmented code of the experiment to list the features for
        analysisProcedureOrNull - The analysis procedure used to filter the result. That is, the result is restricted to feature vector data sets with a value of property ANALYSIS_PROCEDURE as specified. If null (or [] in MatLab) no restriction applies.
        Returns:
        Each row contains information about one feature. Currently the only information available is the feature name.
      • loadDataSets

        public static java.lang.Object[][] loadDataSets​(java.lang.String augmentedPlateCode,
                                                        java.lang.String dataSetTypeCodePattern,
                                                        java.lang.String overrideStoreRootPathOrNull)
        Loads data sets for specified plate code. For each data set the path to the root of the data set is returned. If it is possible the path points directly into the data set store. No data is copied. Otherwise the data is retrieved from the data store server.
        If the same dataset is loaded for the second time in one session it will be immediately returned from the local cache.

        Matlab example:

         % Load all data sets of plate P005 in space SPACE
         dsinfo = OpenBISScreeningML.loadDataSets('/SPACE/P005', 'HCS_ANALYSIS_CELL_FEATURES_CC_MAT', '/mount/openbis-store')
         % Get the data set codes
         dsinfo(:,1)
         % Get root path of first data set (assuming there is at least one)
         dsginfo(1,2)
         % Get the properties for the first data set
         props = dsginfo(1,3)
         % Get property key of first property
         props(1,1)
         % Get property value of first property
         props(1,2)
         % Get all parents of first data set (assuming there is at least one)
         dsInfo(1,4)
         
        Parameters:
        augmentedPlateCode - The augmented plate code.
        dataSetTypeCodePattern - only datasets of the type which matches the specified pattern will be returned. To fetch all datasets specify ".*".
        overrideStoreRootPathOrNull - A path, in the context of the local file system mounts, to the DSS' store root. If null, paths are returned in the context of the DSS' file system mounts.
        Returns:
        Each row contains information about one data set:

        { data set code, data set root path, { {key1, value1}, {key2, value2} ...}, parents }

      • loadDataSets

        public static java.lang.Object[][] loadDataSets​(java.lang.String augmentedPlateCode,
                                                        java.lang.String dataSetTypeCodePattern,
                                                        java.lang.Object[][] properties,
                                                        java.lang.String overrideStoreRootPathOrNull)
        Loads data sets for specified plate code. For each data set the path to the root of the data set is returned. If it is possible the path points directly into the data set store. No data is copied. Otherwise the data is retrieved from the data store server.
        If the same dataset is loaded for the second time in one session it will be immediately returned from the local cache.

        Matlab example:

         % Load all data sets of plate P005 in space SPACE
         properties = {'ANALYSIS_PROCEDURE' 'AX87'}
         dsinfo = OpenBISScreeningML.loadDataSets('/SPACE/P005', 'HCS_ANALYSIS_CELL_FEATURES_CC_MAT', properties, '/mount/openbis-store')
         % Get the data set codes
         dsinfo(:,1)
         % Get root path of first data set (assuming there is at least one)
         dsinfo(1,2)
         % Get the properties for the first data set
         props = dsinfo(1,3)
         % Get property key of first property
         props(1,1)
         % Get property value of first property
         props(1,2)
         % Get all parents of first data set (assuming there is at least one)
         dsInfo(1,4)
         
        Parameters:
        augmentedPlateCode - The augmented plate code.
        dataSetTypeCodePattern - only data sets of the type which matches the specified pattern will be returned. To fetch all data sets specify ".*".
        properties - Only data set with specified property values will be returned. This is a two dimensional array where the first column contains the property codes and the second column the corresponding property values.
        overrideStoreRootPathOrNull - A path, in the context of the local file system mounts, to the DSS' store root. If null, paths are returned in the context of the DSS' file system mounts.

        { data set code, data set root path, { {key1, value1}, {key2, value2} ...}, parents }

        Returns:
        Each row contains information about one data set:
      • loadDataSetsForExperiment

        public static java.lang.Object[][] loadDataSetsForExperiment​(java.lang.String augmentedExperimentCode,
                                                                     java.lang.String dataSetTypeCodePattern,
                                                                     java.lang.Object[][] properties,
                                                                     java.lang.String overrideStoreRootPathOrNull)
        Loads data sets for specified experiment code. For each data set the path to the root of the data set is returned. If it is possible the path points directly into the data set store. No data is copied. Otherwise the data is retrieved from the data store server.
        If the same dataset is loaded for the second time in one session it will be immediately returned from the local cache.

        Matlab example:

         % Load all data sets of experiment E005 in space SPACE and project PROJECT
         properties = {'ANALYSIS_PROCEDURE' 'AX87'}
         dsinfo = OpenBISScreeningML.loadDataSetsForExperiment('/SPACE/PROJECT/E005', 'HCS_ANALYSIS_CELL_FEATURES_CC_MAT', properties, '/mount/openbis-store')
         % Get the data set codes
         dsinfo(:,1)
         % Get root path of first data set (assuming there is at least one)
         dsinfo(1,2)
         % Get the properties for the first data set
         props = dsinfo(1,3)
         % Get property key of first property
         props(1,1)
         % Get property value of first property
         props(1,2)
         % Get all parents of first data set (assuming there is at least one)
         dsInfo(1,4)
         
        Parameters:
        augmentedExperimentCode - The augmented experiment code.
        dataSetTypeCodePattern - only data sets of the type which matches the specified pattern will be returned. To fetch all data sets specify ".*".
        properties - Only data set with specified property values will be returned. This is a two dimensional array where the first column contains the property codes and the second column the corresponding property values.
        overrideStoreRootPathOrNull - A path, in the context of the local file system mounts, to the DSS' store root. If null, paths are returned in the context of the DSS' file system mounts.

        { data set code, data set root path, { {key1, value1}, {key2, value2} ...}, parents }

        Returns:
        Each row contains information about one data set:
      • listDataSetFilesForExperiment

        public static java.lang.Object[][][] listDataSetFilesForExperiment​(java.lang.String augmentedExperimentCode,
                                                                           java.lang.String dataSetTypeCodePattern)
        Lists all files of all data sets for specified experiment and data set type code matching specified regular expression pattern.

        Matlab example:

         % List all data sets of experiment E005 in space SPACE and project PROJECT. The query is restricted to data sets
         % of a type starting with HCS_IMAGE
         files = OpenBISScreeningML.listDataSetFilesForExperiment('/SPACE/PROJECT/E005', 'HCS_IMAGE.*')
         % Codes of all found data sets
         files(:,1)
         % Code of third data set (assuming at least three data sets found)
         files(3,1)
         % Files of third data set (assuming at least three data sets found)
         files(3,2,:)
         
        Parameters:
        augmentedExperimentCode - The augmented experiment code.
        dataSetTypeCodePattern - only data sets of the type which matches the specified pattern will be returned. To fetch all data sets specify ".*".
        Returns:
        {data set code, file/folder paths}
      • getLinkOrCopyOfContents

        protected static java.io.File getLinkOrCopyOfContents​(java.lang.String overrideStoreRootPathOrNull,
                                                              DataSet dataSet,
                                                              java.io.File file)
      • loadDataSetFile

        public static java.lang.Object loadDataSetFile​(java.lang.String dataSetCode,
                                                       java.lang.String pathInDataSet,
                                                       java.lang.String overrideStoreRootPathOrNull)
        Loads file/folder of specified data set and specified file/folder path inside the data set. If it is possible the path points directly into the data set store. No data is copied. Otherwise the data is retrieved from the data store server.

        Matlab example:

         % List all data sets of plate P005 in space SPACE. The query is restricted to data sets
         % of a type starting with HCS_IMAGE
         files = OpenBISScreeningML.listDataSetsFiles('/SPACE/P005', 'HCS_IMAGE.*')
         % Load from the first data set (assuming at least one data set found) the third file/folder 
         % (assuming at least three files/folders)
         file = OpenBISScreeningML.loadDataSetFile(files(1,1), files(1,2,3), [])
         
        Parameters:
        dataSetCode - The code of the data set.
        pathInDataSet - Path inside the data set pointing to the file/folder which should be down loaded. Use '/' if all files are requested.
        overrideStoreRootPathOrNull - A path, in the context of the local file system mounts, to the DSS' store root. If null, paths are returned in the context of the DSS' file system mounts.
        Returns:
        path to the down loaded file/folder.
      • listDataSetsFiles

        public static java.lang.Object[][][] listDataSetsFiles​(java.lang.String augmentedPlateCode,
                                                               java.lang.String dataSetTypeCodePattern)
        Lists all files of all data sets for specifies plate and data set type code matching specified regular expression pattern.

        Matlab example:

         % List all data sets of plate P005 in space SPACE. The query is restricted to data sets
         % of a type starting with HCS_IMAGE
         files = OpenBISScreeningML.listDataSetsFiles('/SPACE/P005', 'HCS_IMAGE.*')
         % Codes of all found data sets
         files(:,1)
         % Code of third data set (assuming at least three data sets found)
         files(3,1)
         % Files of third data set (assuming at least three data sets found)
         files(3,2,:)
         
        Parameters:
        augmentedPlateCode - The augmented plate code.
        dataSetTypeCodePattern - only data sets of the type which matches the specified pattern will be returned. To fetch all data sets specify ".*".
        Returns:
        {data set code, file/folder paths}
      • getDataSetMetaData

        public static java.lang.Object[][][] getDataSetMetaData​(java.lang.String[] dataSetCodes)
        Lists meta data of specified data sets. This includes data set type, properties and codes of connected parent and children data sets. The result is returned in the same order as the data set code array argument.

        Matlab example:

         % List meta data for data sets 20101006020318852-10 and 20110919083636428-236
         metadata = OpenBISScreeningML.getDataSetMetaData({ '20101006020318852-10' '20110919083636428-236'})
         % Codes of all data sets
         metadata(:,1,1)
         % Types of all data sets
         metadata(:,1,2)
         % Properties of first data set
         metadata(1, 2)
         % Parents of second data set
         metadata(2, 3, :)
         % Children of first data set
         metadata(1, 4, :)
         
        Parameters:
        dataSetCodes - Codes of data sets from whom meta data are queried.
        Returns:
        For each data set: {{data set code, data set type}, { {key1, value1}, {key2, value2} ...}, parents, children }
      • uploadDataSet

        public static java.lang.Object uploadDataSet​(java.lang.String augmentedPlateCode,
                                                     java.lang.String dataSetFilePath,
                                                     java.lang.String dataSetType,
                                                     java.lang.Object[][] dataSetProperties)
        Uploads specified data set for specified plate. The data set code will be returned.

        Matlab example:

         % Upload data set /path/to/my-data-set with properties DESCRIPTION and NUMBER for 
         % plate P005 in space SPACE
         properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
         datasetcode = OpenBISScreeningML.uploadDataSet('/SPACE/P005', '/path/to/my-data-set', 'HCS_IMAGE', properties)
         
        Parameters:
        augmentedPlateCode - The augmented plate code.
        dataSetFilePath - Path to the data set file/folder to be uploaded.
        dataSetType - Data set type.
        dataSetProperties - A two dimensional array where the first column contains the property codes and the second column the corresponding property values.
      • uploadDataSetForPlateAndParents

        public static java.lang.Object uploadDataSetForPlateAndParents​(java.lang.String augmentedPlateCode,
                                                                       java.lang.Object[] parentDataSetCodeObjects,
                                                                       java.lang.String dataSetFilePath,
                                                                       java.lang.String dataSetType,
                                                                       java.lang.Object[][] dataSetProperties)
        Uploads specified data set for specified plate. The data set code will be returned.

        Matlab example:

         % Upload data set /path/to/my-data-set with properties DESCRIPTION and NUMBER for 
         % plate P005 in space SPACE
         % with data set  201007091122-928 as the parent
         properties = {'DESCRIPTION' 'hello example'; 'NUMBER' 3.14}
         parents = {'201007091122-928' }
         datasetcode = OpenBISScreeningML.uploadDataSetForPlateAndParents('/SPACE/P005', parents, '/path/to/my-data-set', 'HCS_IMAGE', properties)
         
        Parameters:
        augmentedPlateCode - The augmented plate code.
        parentDataSetCodeObjects - The codes of the parents of this data set
        dataSetFilePath - Path to the data set file/folder to be uploaded.
        dataSetType - Data set type.
        dataSetProperties - A two dimensional array where the first column contains the property codes and the second column the corresponding property values.
      • uploadDataSetForExperimentAndParents

        public static java.lang.Object uploadDataSetForExperimentAndParents​(java.lang.String augmentedExperimentCode,
                                                                            java.lang.Object[] parentDataSetCodeObjects,
                                                                            java.lang.String dataSetFilePath,
                                                                            java.lang.String dataSetType,
                                                                            java.lang.Object[][] dataSetProperties)
        Uploads a data set to the specified experiment, setting the data set parents. The data set code will be returned.

        Matlab example:

         % Upload data set /path/to/my-data-set (with property DESCRIPTION)
         % to experiment E103 in project PROJECT and space SPACE,
         % with data set  201007091122-928 as the parent
         properties = {'DESCRIPTION' 'hello example' }
         parents = {'201007091122-928' }
         datasetcode = OpenBISScreeningML.uploadDataSetForExperimentAndParents('/SPACE/PROJECT/E103', parents, '/path/to/my-data-set', 'HCS_IMAGE', properties)
         
        Parameters:
        augmentedExperimentCode - The augmented experiment code.
        parentDataSetCodeObjects - The codes of the parents of this data set
        dataSetFilePath - Path to the data set file/folder to be uploaded.
        dataSetType - Data set type.
        dataSetProperties - A two dimensional array where the first column contains the property codes and the second column the corresponding property values.
      • loadImages

        public static java.lang.Object[][][] loadImages​(java.lang.String plate,
                                                        int row,
                                                        int col)
        Loads the TIFF images for the given well location, all tiles and all channels and stores them in temporary files. The temporary files will be removed automatically when the Java Virtual Machine exits.

        Matlab example:

         % Load the images for all channels of well B10 of plate P005 in space SPACE
         imginfo = OpenBISScreeningML.loadImages('/SPACE/P005', 2, 10)
         % Get the plate-well descriptions of all locations
         imginfo(2,:,3)
         % Show the third image (assuming there are at least three images)
         imtool(imginfo(1,3))
         
        Parameters:
        plate - The augmented plate code
        row - The row in the plate to get the images for
        col - The column in the plate to get the images for
        Returns:
        { names of TIFF files, image annotation }

        Each of names of TIFF files and image annotation is a vector of length of the number of images.

        image annotation contains { channel name, tile number, plate well description, plate augmented code, plate perm id, plate space code, plate code, row, column, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code, data set code }

      • loadImages

        public static java.lang.Object[][][] loadImages​(java.lang.String plate,
                                                        int row,
                                                        int col,
                                                        int tile)
        Loads the TIFF images for the given well location, tile number, and all channels and stores them in temporary files. The temporary files will be removed automatically when the Java Virtual Machine exits.

        Matlab example:

         % Load the images for all channels of well B10 and tile 3 of plate P005 in space SPACE
         imginfo = OpenBISScreeningML.loadImages('/SPACE/P005', 2, 10, 3)
         % Get the plate-well descriptions of all locations
         imginfo(2,:,3)
         % Show the third image (assuming there are at least three images)
         imtool(imginfo(1,3))
         
        Parameters:
        plate - The augmented plate code
        row - The row in the plate to get the images for
        col - The column in the plate to get the images for
        tile - The tile number. Starts with 0.
        Returns:
        { names of TIFF files, image annotation }

        Each of names of TIFF files and image annotation is a vector of length of the number of images.

        image annotation contains { channel name, tile number, plate well description, plate augmented code, plate perm id, plate space code, plate code, row, column, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code, data set code }

      • loadImages

        public static java.lang.Object[][][] loadImages​(java.lang.String plate,
                                                        int row,
                                                        int col,
                                                        java.lang.String[] channels)
        Loads the TIFF images for the given well location, list of channels, and all tiles and stores them in temporary files. The temporary files will be removed automatically when the Java Virtual Machine exits.

        Matlab example:

         % Load the images for channel DAPI of well H10 of plate P005 in space SPACE
         imginfo=OpenBISScreeningML.loadImages('/SPACE/P005', 8, 10, 'DAPI')
         % Get the channel names and tile numbers of all locations
         imginfo(2,:,1:2)
         % Show the second image (assuming there are at least two images)
         imtool(imginfo(1,2))
         
        Parameters:
        plate - The augmented plate code
        row - The row in the plate to get the images for
        col - The column in the plate to get the images for
        channels - The names of the channels to get the images for
        Returns:
        { names of TIFF files, image annotation }

        Each of names of TIFF files and image annotation is a vector of length of the number of images.

        image annotation contains { channel name, tile number, plate well description, plate augmented code, plate perm id, plate space code, plate code, row, column, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code, data set code }

      • loadSegmentationImages

        public static java.lang.Object[][][] loadSegmentationImages​(java.lang.String plate,
                                                                    int row,
                                                                    int col,
                                                                    java.lang.String[] objectNamesOrNull,
                                                                    java.lang.String analysisProcedureOrNull)
        Has the same effect as loadImages(String, int, int, String[]), but instead of loading raw images loads their segmentation results if available.
        Parameters:
        objectNamesOrNull - The names of the segmentation objects to get the images for. If null (or [] in MatLab) no restriction applies.
        analysisProcedureOrNull - The analysis procedure used to filter the result. That is, the result is restricted to feature vector data sets with a value of property ANALYSIS_PROCEDURE as specified. If null (or [] in MatLab) no restriction applies.
      • loadImages

        public static java.lang.Object[][][] loadImages​(java.lang.String plate,
                                                        int row,
                                                        int col,
                                                        int tile,
                                                        java.lang.String[] channels)
        Loads the TIFF images for the given well location, tile number, and list of channels and stores them in temporary files. The temporary files will be removed automatically when the Java Virtual Machine exits.

        Matlab example:

         % Load the images for channel DAPI of well H10 and tile 3 of plate P005 in space SPACE
         imginfo=OpenBISScreeningML.loadImages('/SPACE/P005', 8, 10, 3, 'DAPI')
         % Get the channel names of all locations
         imginfo(2,:,1)
         % Show the second image (assuming there are at least two images)
         imtool(imginfo(1,2))
         
        Parameters:
        plate - The augmented plate code
        row - The row in the plate to get the images for
        col - The column in the plate to get the images for
        tile - The tile number. Starts with 0.
        channels - The names of the channels to get the images for
        Returns:
        { names of TIFF files, image annotation }

        Each of names of TIFF files and image annotation is a vector of length of the number of images.

        image annotation contains { channel name, tile number, plate well description, plate augmented code, plate perm id, plate space code, plate code, row, column, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code, data set code }

      • loadSegmentationImages

        public static java.lang.Object[][][] loadSegmentationImages​(java.lang.String plate,
                                                                    int row,
                                                                    int col,
                                                                    int tile,
                                                                    java.lang.String[] objectNamesOrNull,
                                                                    java.lang.String analysisProcedureOrNull)
        Has the same effect as loadImages(String, int, int, int, String[]), but instead of loading raw images loads their segmentation results if available.
        Parameters:
        objectNamesOrNull - The names of the segmentation objects to get the images for. If null (or [] in MatLab) no restriction applies.
        analysisProcedureOrNull - The analysis procedure used to filter the result. That is, the result is restricted to feature vector data sets with a value of property ANALYSIS_PROCEDURE as specified. If null (or [] in MatLab) no restriction applies.
      • listSegmentationObjects

        public static java.lang.Object[][] listSegmentationObjects​(java.lang.String plate,
                                                                   java.lang.String analysisProcedureOrNull)
        Lists all segmentation objects for the plate.

        Matlab example:

         % Get the segmentation objects of plate P005 in space SPACE.
         segmentationObjects = OpenBISScreeningML.listSegmentationObjects('/SPACE/P005', []);
         % Get the segmentation objects of plate P005 in space SPACE for data sets calculated 
         % with analysis procedure AP-42.
         segmentationObjects = OpenBISScreeningML.listSegmentationObjects('/SPACE/P005', 'AP-42');
         % How many segmentation objects do we have?
         length(segmentationObjects)
         % What is the name of segmentation objects 1?
         segmentationObjects(1)
         
        Parameters:
        plate - augmented code of the plate
        analysisProcedureOrNull - The analysis procedure used to filter the result. That is, the result is restricted to feature vector data sets with a value of property ANALYSIS_PROCEDURE as specified. If null (or [] in MatLab) no restriction applies.
        Returns:
        Each row contains information about one segmentation object. Currently the only information available is the segmentation object name.
      • getFeatureMatrix

        public static java.lang.Object[][][][] getFeatureMatrix​(java.lang.String experiment,
                                                                java.lang.String gene,
                                                                java.lang.String analysisProcedureOrNull,
                                                                java.lang.String[] featuresOrNull)
        Returns the feature matrix of the specified features for all locations in experiment (a location is one well position in one feature vector data set) in experiment connected to gene in [0], location annotations in [1] and feature annotation in [2].

        Matlab example:

         % Get feature matrix for experiment /SPACE/PROJ/MYEXP for locations connected to GENENAME
         fmatrix = OpenBISScreeningML.getFeatureMatrix('/SPACE/PROJ/MYEXP', 'GENENAME', [], []);
         % Get feature matrix for features F1, F2 and F3 for 
         % experiment /SPACE/PROJ/MYEXP for locations connected to GENENAME
         fmatrix = OpenBISScreeningML.getFeatureMatrix('/SPACE/PROJ/MYEXP', 'GENENAME', [], {'F1' 'F2' 'F3'));
         % Get feature matrix for features F1 and F2 for experiment /SPACE/PROJ/MYEXP for locations 
         % connected to GENENAME calculated with analysis procedure AP-42.
         fmatrix = OpenBISScreeningML.getFeatureMatrix('/SPACE/PROJ/MYEXP', 'GENENAME', 'AP-42', {'F1' 'F2'));
         % Get the feature vector for the second location (assuming that there are at least two locations) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(1,:,2,3)
         % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(1,4,:,3)
         % Get code of the fourth feature (assuming that there are at least 4 features)
         fmatrix(3,4)
         % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(2,2,3,:)
         
        Parameters:
        experiment - The augmented experiment code
        gene - The gene code (stored as material code in openBIS, usually it is gene id)
        analysisProcedureOrNull - The code of the analysis procedure used to calculate requested features. That is, the result is restricted to feature vector data sets with a value of property ANALYSIS_PROCEDURE as specified. If null (or [] in MatLab) no restriction applies.
        featuresOrNull - The codes of the features to contain the feature matrix. Unknown feature codes will be ignored. If null (or [] in MatLab) all features are returned.
        Returns:
        a four dimensional matrix. The first dimension denotes the type in the following order: {feature matrix, annotations per location, feature codes}. The other dimensions depend on the value of the first dimension:
        1. feature matrix: 2. dimension is feature vector, 3. dimension is location number, 4. dimension is data set number. If for a particular location and a particular data set the corresponding feature value does not exists NaN will be returned.
        2. annotations: 2. dimension is location number, 3. dimension is data set number, 4. dimension is location annotations in the following order: {plate well description, plate augmented code, plate perm id, plate space code, plate code, row, column, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code, data set code, data set type}
        3. feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4. dimension are meaningless (i.e. they have length one)
      • getFeatureMatrix

        public static java.lang.Object[][][][] getFeatureMatrix​(java.lang.String gene,
                                                                java.lang.String analysisProcedureOrNull,
                                                                java.lang.String[] featuresOrNull)
        Returns the feature matrix of the specified features for all locations (a location is one well position in one feature vector data set) in experiment connected to gene in [0], location annotations in [1] and feature annotation in [2].

        Matlab example:

         % Get feature matrix for GENENAME
         fmatrix = OpenBISScreeningML.getFeatureMatrix('GENENAME', [], []);
         % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE3 for GENENAME
         fmatrix = OpenBISScreeningML.getFeatureMatrix('GENENAME', [], {'FEATURE1' 'FEATURE2' 'FEATURE3'});
         % Get feature matrix for features FEATURE1 and FEATURE2 for GENENAME 
         % computed with analysis procedure AP-42
         fmatrix = OpenBISScreeningML.getFeatureMatrix('GENENAME', 'AP-42', {'FEATURE1' 'FEATURE2'});
         % Get the feature vector for the second location (assuming that there are at least two locations) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(1,:,2,3)
         % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(1,4,:,3)
         % Get code of the fourth feature (assuming that there are at least 4 features)
         fmatrix(3,4)
         % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(2,2,3,:)
         
        Parameters:
        gene - The gene code (stored as material code in openBIS, usually it is gene id)
        analysisProcedureOrNull - The code of the analysis procedure used to calculate requested features. That is, the result is restricted to feature vector data sets with a value of property ANALYSIS_PROCEDURE as specified. If null (or [] in MatLab) no restriction applies.
        featuresOrNull - The codes of the features to contain the feature matrix. Unknown feature codes will be ignored. If null (or [] in MatLab) all features are returned.
        Returns:
        a four dimensional matrix. The first dimension denotes the type in the following order: {feature matrix, annotations per location, feature codes}. The other dimensions depend on the value of the first dimension:
        1. feature matrix: 2. dimension is feature vector, 3. dimension is location number, 4. dimension is data set number. If for a particular location and a particular data set the corresponding feature value does not exists NaN will be returned.
        2. annotations: 2. dimension is location number, 3. dimension is data set number, 4. dimension is location annotations in the following order: {plate well description, plate augmented code, plate perm id, plate space code, plate code, row, column, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code, data set code, data set type}
        3. feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4. dimension are meaningless (i.e. they have length one)
      • getFeatureMatrixForPlate

        public static java.lang.Object[][][][] getFeatureMatrixForPlate​(java.lang.String plate,
                                                                        java.lang.String analysisProcedureOrNull,
                                                                        java.lang.String[] featuresOrNull)
        Returns the feature matrix of the specified features for all locations (a location is one well position in one feature vector data set) of all feature vector data sets created by specified analysis procedure of the given plate in [0], location annotations in [1] and feature annotation in [2].

        Matlab example:

         % Get feature matrix for PLATECODE
         fmatrix = OpenBISScreeningML.getFeatureMatrixForPlate('PLATECODE', [], []);
         % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE3 for PLATECODE.
         fmatrix = OpenBISScreeningML.getFeatureMatrixForPlate('PLATECODE', [], {'FEATURE1' 'FEATURE2' 'FEATURE3'});
         % Get feature matrix for features FEATURE1 and FEATURE2 for PLATECODE calculated by analysis procedure AP-42.
         fmatrix = OpenBISScreeningML.getFeatureMatrixForPlate('PLATECODE', 'AP-42', {'FEATURE1' 'FEATURE2'});
         % Get the feature vector for the second location (assuming that there are at least two locations) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(1,:,2,3)
         % Get the values of the fourth feature for all locations (assuming that there are at least 4 features) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(1,4,:,3)
         % Get code of the fourth feature (assuming that there are at least 4 features)
         fmatrix(3,4)
         % Get the plate-well descriptions for the second location (assuming that there are at least two locations) 
         % of third data set (assuming that there are at least three data sets)
         fmatrix(2,2,3,:)
         
        Parameters:
        plate - augmented code of the plate for which features should be loaded
        analysisProcedureOrNull - The code of the analysis procedure used to calculate requested features. That is, the result is restricted to feature vector data sets with a value of property ANALYSIS_PROCEDURE as specified. If null (or [] in MatLab) no restriction applies.
        featuresOrNull - The codes of the features to contain the feature matrix. Unknown feature codes will be ignored. If null (or [] in MatLab) all features are returned.
        Returns:
        a four dimensional matrix. The first dimension denotes the type in the following order: {feature matrix, annotations per location, feature codes}. The other dimensions depend on the value of the first dimension:
        1. feature matrix: 2. dimension is feature vector, 3. dimension is location number, 4. dimension is data set number. If for a particular location and a particular data set the corresponding feature value does not exists NaN will be returned.
        2. annotations: 2. dimension is location number, 3. dimension is data set number, 4. dimension is location annotations in the following order: {plate well description, plate augmented code, plate perm id, plate space code, plate code, row, column, experiment augmented code, experiment perm id, experiment space code, experiment project code, experiment code, data set code, data set type}
        3. feature codes: 2. dimension is feature codes in alphabetical order. 3. and 4. dimension are meaningless (i.e. they have length one)
      • getGeneMappingForPlates

        public static java.lang.Object[][][] getGeneMappingForPlates​(java.lang.String[] platesCodes)
        Returns the gene mapping for the given plateCodes in [0] and location annotations in [1].

        One row in the matrix corresponds to one well.

        Matlab example:

         % Get feature matrix for features FEATURE1, FEATURE2 and FEATURE for PLATECODE
         genes = getGeneMappingForPlate('PLATECODE');
         % Get the plate well location description of the 10th wells
         loc2 = genes(2,10,1)
         % Get the gene ids that are in the 10th well
         geneIds = genes(1,10,:)
         
        Parameters:
        platesCodes - The augmented codes of the plates to get the mapping for
        Returns:
        { gene ids, annotations per well } where gene ids can be 0, 1 or more gene ids. annotations per location contain:

        { plate well description, plate augmented code, plate perm id, plate space code, plate code, row, column }

      • getPlateMetadataList

        public static PlateMetadata[] getPlateMetadataList​(java.lang.String[] platesCodes)
        Experimental method that returns an array of PlateMetadata Java objects for a given list of plate codes.

         chosenPlates= { '/MY-SPACE/MY-PLATE1', '/MY-SPACE/MY-PLATE2' };
         metadata = OpenBISScreeningML.getPlateMetadataList(chosenPlates);
         % List all methods available on the result:
         methods(metadata(1),'-full');
         % Lists all wells of the first plate
         javaMethod('getWells',metadata(1))
         % Shows plate geometry of the first plate
         javaMethod('getPlateGeometry',metadata(1))
         
      • getContainerDataSetCode

        public static java.lang.String getContainerDataSetCode​(java.lang.String dataSetCode)