Package ome.services.blitz.repo

Interface RepositoryDao

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      boolean canUpdate​(IObject obj, Ice.Current current)
      Delegates to IAdmin#canUpdate
      void createOrFixUserDir​(java.lang.String uuid, java.util.List<CheckedPath> path, org.hibernate.Session s, ome.system.ServiceFactory sf, ome.util.SqlAction sql)
      Checks that the given CheckedPath objects exist (via findRepoFile(String, CheckedPath, String, Ice.Current)) and are in the "user" group.
      java.util.List<java.lang.Integer> deleteRepoDeleteLogs​(java.util.List<ome.util.SqlAction.DeleteLog> templates, Ice.Current current)
      Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context for a number of templates.
      int deleteRepoDeleteLogs​(ome.util.SqlAction.DeleteLog template, Ice.Current current)
      Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context.
      java.util.List<java.lang.Long> filterFilesByRepository​(java.lang.String repo, java.util.List<java.lang.Long> ids, Ice.Current current)
      Find the original file IDs among those given that are in the given repository.
      java.util.List<java.util.List<ome.util.SqlAction.DeleteLog>> findRepoDeleteLogs​(java.util.List<ome.util.SqlAction.DeleteLog> templates, Ice.Current current)
      As findRepoDeleteLogs(DeleteLog, Current) but for a collection of templates.
      java.util.List<ome.util.SqlAction.DeleteLog> findRepoDeleteLogs​(ome.util.SqlAction.DeleteLog template, Ice.Current current)
      Call SqlAction.findRepoDeleteLogs(DeleteLog) with the current context.
      OriginalFile findRepoFile​(java.lang.String uuid, CheckedPath checked, java.lang.String mimetype, Ice.Current current)
      Delegate to SqlAction.findRepoFile(String, String, String, String) for looking up the id of the file, and then load it normally via IQuery.
      ome.model.core.OriginalFile findRepoFile​(ome.system.ServiceFactory sf, ome.util.SqlAction sql, java.lang.String uuid, CheckedPath checked, java.lang.String mimetype)
      As findRepoFile(String, CheckedPath, String, Current) but can be called from within a transaction.
      ome.model.enums.ChecksumAlgorithm getChecksumAlgorithm​(java.lang.String name, Ice.Current current)
      Retrieve the checksum algorithm of the given name.
      EventContext getEventContext​(Ice.Current current)
      Look up information for the current session as specified in the ctx field of the current.
      FsFile getFile​(long id, Ice.Current current, java.lang.String repoUuid)
      Get an FsFile object based on its ID.
      OriginalFile getOriginalFile​(long fileId, Ice.Current current)
      Gets the original file instance for a given file ID.
      java.util.List<OriginalFile> getOriginalFiles​(java.lang.String repoUuid, CheckedPath checked, Ice.Current current)
      Return a non-null, possibly empty list of OriginalFile elements which are accessible to the given user at the given path.
      ome.model.core.OriginalFile getOriginalFileWithHasher​(long id, Ice.Current current)
      Retrieve the original file of the given ID.
      ome.api.RawFileStore getRawFileStore​(long fileId, CheckedPath checked, java.lang.String mode, Ice.Current current)
      Create a RawFileBean (i.e.
      java.lang.String getUserInstitution​(long userId, Ice.Current current)
      Get the current user's institution.
      java.lang.String getUserInstitution​(long userId, ome.system.ServiceFactory sf)
      Get the current user's institution.
      java.util.List<Fileset> loadFilesets​(java.util.List<java.lang.Long> ids, Ice.Current current)
      Load filesets by id.
      void makeDirs​(PublicRepositoryI repo, java.util.List<CheckedPath> dirs, boolean parents, Ice.Current c)
      Create a number of directories in a single transaction, using the PublicRepositoryI instance as a callback for implementation specific logic.
      OriginalFile register​(java.lang.String repoUuid, CheckedPath checked, java.lang.String mimetype, Ice.Current current)
      Register an OriginalFile object
      ome.model.core.OriginalFile register​(java.lang.String repoUuid, CheckedPath checked, java.lang.String mimetype, ome.system.ServiceFactory sf, ome.util.SqlAction sql, org.hibernate.Session session)
      Like register(String, CheckedPath, String, Ice.Current) but does not create a new transaction.
      Fileset saveFileset​(java.lang.String repoUuid, Fileset fs, ChecksumAlgorithm checksumAlgorithm, java.util.List<CheckedPath> paths, Ice.Current current)
      Fill the various fields of the Fileset and then save the entire instance into the database.
      <T extends Job>
      T      		 saveJob​(T job, Ice.Current current)
      Create a job from an instance provided by either the client or the server.
      void saveObject​(ome.model.IObject object, Ice.Current current)
      Save the given model object.
      RMap treeList​(java.lang.String repoUuid, CheckedPath checked, Ice.Current __current)  
      void updateJob​(Job job, java.lang.String message, java.lang.String status, Ice.Current current)
      Set both the message and the status of the given job.

    • Method Detail

      • getRawFileStore

        ome.api.RawFileStore getRawFileStore​(long fileId,
                                     CheckedPath checked,
                                     java.lang.String mode,
                                     Ice.Current current)
                              throws SecurityViolation
        Create a RawFileBean (i.e. an implementation of RawFileStore which can be passed to RepoRawFileStoreI for performing internal functions. The primary difference to an instance created via the ServiceFactory is that the RawFileBean.setFileIdWithBuffer(long, FileBuffer) method is called pointing to a non-romio file path, e.g. /OMERO/Files/x.
        Parameters:
        fileId - ID of an OriginalFile
        checked - Not null. Normalized path from the repository.
        mode - FileChannel mode, "r", "rw", etc.
        Returns:
        An instance with RawFileBean.setFileIdWithBuffer(long, FileBuffer) called.
        Throws:
        SecurityViolation

      • findRepoFile

        OriginalFile findRepoFile​(java.lang.String uuid,
                          CheckedPath checked,
                          java.lang.String mimetype,
                          Ice.Current current)
                   throws ServerError
        Delegate to SqlAction.findRepoFile(String, String, String, String) for looking up the id of the file, and then load it normally via IQuery. This will enforce any read security checks.
        Parameters:
        uuid -
        checked -
        mimetype -
        current -
        Returns:
        See above.
        Throws:
        ServerError

      • canUpdate

        boolean canUpdate​(IObject obj,
                  Ice.Current current)
        Delegates to IAdmin#canUpdate
        Parameters:
        obj -
        current -
        Returns:
        See above.
        Throws:
        an - SecurityViolation if the currentUser is not allowed to access the given file.

      • filterFilesByRepository

        java.util.List<java.lang.Long> filterFilesByRepository​(java.lang.String repo,
                                                       java.util.List<java.lang.Long> ids,
                                                       Ice.Current current)
        Find the original file IDs among those given that are in the given repository.
        Parameters:
        repo - a repository UUID
        ids - IDs of original files
        current - Ice method invocation context
        Returns:
        those IDs among those given whose original files are in the given repository

      • getOriginalFile

        OriginalFile getOriginalFile​(long fileId,
                             Ice.Current current)
                      throws SecurityViolation
        Gets the original file instance for a given file ID.
        Parameters:
        fileId - a file ID
        current - applicable ICE context
        Returns:
        the original file corresponding to the given file ID
        Throws:
        SecurityViolation - if the query threw a security violation

      • getOriginalFiles

        java.util.List<OriginalFile> getOriginalFiles​(java.lang.String repoUuid,
                                              CheckedPath checked,
                                              Ice.Current current)
                                       throws SecurityViolation
        Return a non-null, possibly empty list of OriginalFile elements which are accessible to the given user at the given path. If the directory which they are associated with is not also readable by the current user, then a SecurityViolation will be thrown.
        Parameters:
        repoUuid - for the repository in question.
        checked - normalized path which can be found as the value of OriginalFile.getPath() in the database.
        current -
        Throws:
        SecurityViolation

      • saveFileset

        Fileset saveFileset​(java.lang.String repoUuid,
                    Fileset fs,
                    ChecksumAlgorithm checksumAlgorithm,
                    java.util.List<CheckedPath> paths,
                    Ice.Current current)
             throws ServerError
        Fill the various fields of the Fileset and then save the entire instance into the database.
        Parameters:
        repoUuid - for the repository in question.
        fs - a user provided Fileset that must minimally have the FilesetEntry objects present with their clientPath set. The rest of the fields will be filled here.
        checksumAlgorithm - The algorithm to use.
        paths - a List of the same size as the number of entries in fs one per FilesetEntry.
        current - Current context
        Throws:
        ServerError

      • loadFilesets

        java.util.List<Fileset> loadFilesets​(java.util.List<java.lang.Long> ids,
                                     Ice.Current current)
                              throws ServerError
        Load filesets by id.
        Parameters:
        ids -
        current -
        Returns:
        See above.
        Throws:
        ServerError

      • register

        OriginalFile register​(java.lang.String repoUuid,
                      CheckedPath checked,
                      java.lang.String mimetype,
                      Ice.Current current)
               throws ServerError
        Register an OriginalFile object
        Parameters:
        repoUuid - uuid of the repository that the given file argument should be registered with. Cannot be null.
        checked - Normalized path provided by the repository. Not null.
        mimetype - Mimetype for use with the OriginalFile. May be null in which case a default will be chosen.
        current - Not null.
        Returns:
        The OriginalFile with id set (unloaded)
        Throws:
        ServerError

      • register

        ome.model.core.OriginalFile register​(java.lang.String repoUuid,
                                     CheckedPath checked,
                                     java.lang.String mimetype,
                                     ome.system.ServiceFactory sf,
                                     ome.util.SqlAction sql,
                                     org.hibernate.Session session)
                              throws ServerError
        Like register(String, CheckedPath, String, Ice.Current) but does not create a new transaction. Instead, the ServiceFactory and SqlAction must be passed in. The returned OriginalFile instance is still connected to Hibernate.
        Parameters:
        repoUuid -
        checked -
        mimetype -
        sf -
        sql -
        session -
        Returns:
        See above.
        Throws:
        ServerError

      • getFile

        FsFile getFile​(long id,
               Ice.Current current,
               java.lang.String repoUuid)
        Get an FsFile object based on its ID. Returns null if the file does not exist or does not belong to this repository.
        Parameters:
        id - database ID of the sought original file
        current - current applicable ICE context
        repoUuid - the UUID of the repository containing the original file
        Returns:
        the requested FsFile object

      • saveJob

        <T extends Job> T saveJob​(T job,
                          Ice.Current current)
                   throws ServerError
        Create a job from an instance provided by either the client or the server. Only those fields which are modifiable by the user will be copied.
        Parameters:
        job - Not null.
        current - Not null.
        Returns:
        See above.
        Throws:
        ServerError

      • updateJob

        void updateJob​(Job job,
               java.lang.String message,
               java.lang.String status,
               Ice.Current current)
        throws ServerError
        Set both the message and the status of the given job.
        Parameters:
        job - Not null.
        message - If null, no modification will be made for the message
        status - If null, no modification will be made for the status.
        current - Not null.
        Throws:
        ServerError

      • getEventContext

        EventContext getEventContext​(Ice.Current current)
        Look up information for the current session as specified in the ctx field of the current.

      • getUserInstitution

        java.lang.String getUserInstitution​(long userId,
                                    Ice.Current current)
        Get the current user's institution.
        Parameters:
        userId - the ID of the user whose institution is to be fetched
        current - the current ICE method invocation context
        Returns:
        the institution, may be null

      • getUserInstitution

        java.lang.String getUserInstitution​(long userId,
                                    ome.system.ServiceFactory sf)
        Get the current user's institution.
        Parameters:
        userId - the ID of the user whose institution is to be fetched
        sf - the service factory to use for the query
        Returns:
        the institution, may be null

      • findRepoDeleteLogs

        java.util.List<ome.util.SqlAction.DeleteLog> findRepoDeleteLogs​(ome.util.SqlAction.DeleteLog template,
                                                                Ice.Current current)
        Call SqlAction.findRepoDeleteLogs(DeleteLog) with the current context.
        Parameters:
        template - not null.
        current - not null.
        Returns:
        all the rows found which match the non-null fields on templates

      • findRepoDeleteLogs

        java.util.List<java.util.List<ome.util.SqlAction.DeleteLog>> findRepoDeleteLogs​(java.util.List<ome.util.SqlAction.DeleteLog> templates,
                                                                                Ice.Current current)
        As findRepoDeleteLogs(DeleteLog, Current) but for a collection of templates.
        Parameters:
        templates - not null.
        current - not null.
        Returns:
        all the rows found which match the non-null fields on templates

      • deleteRepoDeleteLogs

        int deleteRepoDeleteLogs​(ome.util.SqlAction.DeleteLog template,
                         Ice.Current current)
        Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context.
        Parameters:
        template - not null.
        current - not null.
        Returns:
        the number of rows deleted

      • deleteRepoDeleteLogs

        java.util.List<java.lang.Integer> deleteRepoDeleteLogs​(java.util.List<ome.util.SqlAction.DeleteLog> templates,
                                                       Ice.Current current)
        Call SqlAction.deleteRepoDeleteLogs(DeleteLog) with the current context for a number of templates.
        Parameters:
        templates - not null.
        current - not null.
        Returns:
        A list containing the number of rows deleted

      • getChecksumAlgorithm

        ome.model.enums.ChecksumAlgorithm getChecksumAlgorithm​(java.lang.String name,
                                                       Ice.Current current)
        Retrieve the checksum algorithm of the given name.
        Parameters:
        name - a checksum algorithm name, must exist
        current - Ice method invocation context
        Returns:
        the corresponding checksum algorithm model object

      • getOriginalFileWithHasher

        ome.model.core.OriginalFile getOriginalFileWithHasher​(long id,
                                                      Ice.Current current)
        Retrieve the original file of the given ID.
        Parameters:
        id - the ID of an original file, must exist
        current - Ice method invocation context
        Returns:
        the corresponding original file model object

      • saveObject

        void saveObject​(ome.model.IObject object,
                Ice.Current current)
        Save the given model object.
        Parameters:
        object - a model object
        current - Ice method invocation context