Package ome.services.blitz.repo

Class PublicRepositoryI

  • All Implemented Interfaces:
    _RepositoryOperations, org.springframework.beans.factory.Aware, org.springframework.context.ApplicationContextAware
    Direct Known Subclasses:
    ManagedRepositoryI
    public class PublicRepositoryI
extends java.lang.Object
implements _RepositoryOperations, org.springframework.context.ApplicationContextAware
    An implementation of the PublicRepository interface.

    • Constructor Summary

      Constructors 
      Constructor Description
      PublicRepositoryI​(RepositoryDao repositoryDao, ome.util.checksum.ChecksumProviderFactory checksumProviderFactory, java.lang.String checksumAlgorithmSupported, java.lang.String pathRules)  

    • Method Summary

      All Methods Instance Methods Concrete Methods Deprecated Methods 
      Modifier and Type Method Description
      protected CheckedPath checkPath​(java.lang.String path, ChecksumAlgorithm checksumAlgorithm, Ice.Current curr)
      Create a new CheckedPath object based on the given user input.
      protected RawFileStorePrx createRepoRFS​(CheckedPath checked, java.lang.String mode, Ice.Current __current)
      Create, initialize, and register an RepoRawFileStoreI with the proper setting (read or write).
      HandlePrx deletePaths​(java.lang.String[] files, boolean recursive, boolean force, Ice.Current __current)
      Delete paths recursively as described in Repositories.ice.
      RawFileStorePrx file​(java.lang.String path, java.lang.String mode, Ice.Current __current)
      Returns a special RawFileStore which permits only the operations set out in the options string ""wb"", ""a+"", etc.
      RawFileStorePrx fileById​(long fileId, Ice.Current __current)  
      boolean fileExists​(java.lang.String path, Ice.Current __current)
      Returns true if the file or path exists within the repository.
      protected OriginalFile findInDb​(CheckedPath checked, java.lang.String mode, Ice.Current current)
      Find the given path in the DB or create.
      protected OriginalFile findOrCreateInDb​(CheckedPath checked, java.lang.String mode, Ice.Current curr)  
      protected OriginalFile findOrCreateInDb​(CheckedPath checked, java.lang.String mode, java.lang.String mimetype, Ice.Current curr)  
      protected Ice.ObjectFactory getFactory​(java.lang.String id, Ice.Current current)  
      java.lang.String getRepoUuid()  
      void initialize​(FileMaker fileMaker, java.lang.Long id, java.lang.String repoUuid)
      Called by the internal repository once initialization has taken place.
      java.util.List<java.lang.String> list​(java.lang.String path, Ice.Current __current)
      Returns a set of strings naming the files and directories in the directory denoted by an abstract pathname.
      java.util.List<OriginalFile> listFiles​(java.lang.String path, Ice.Current __current)
      Returns an array of abstract pathname objects denoting the files in the directory denoted by an abstract pathname.
      protected Ice.Current makeAdjustedCurrent​(Ice.Current __current)  
      protected void makeCheckedDirs​(java.util.LinkedList<CheckedPath> paths, boolean parents, org.hibernate.Session s, ome.system.ServiceFactory sf, ome.util.SqlAction sql, ome.system.EventContext effectiveEventContext)
      Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
      protected void makeCheckedDirs​(java.util.LinkedList<CheckedPath> paths, boolean parents, org.hibernate.Session s, ome.system.ServiceFactory sf, ome.util.SqlAction sql, ome.system.EventContext effectiveEventContext, java.util.function.Consumer<CheckedPath> fileCreationListener)
      Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
      void makeDir​(java.lang.String path, boolean parents, Ice.Current current)
      Create a nested path in the repository.
      void makeDir​(CheckedPath checked, boolean parents, org.hibernate.Session s, ome.system.ServiceFactory sf, ome.util.SqlAction sql, ome.system.EventContext effectiveEventContext)  
      java.lang.String mimetype​(java.lang.String path, Ice.Current __current)
      Get the mimetype for a file.
      protected ome.model.core.OriginalFile persistLogFile​(ome.model.core.OriginalFile originalFile, Ice.Current current)
      Deprecated.
      protected void publishMessage​(ome.util.messages.InternalMessage msg)  
      OriginalFile register​(java.lang.String path, RString mimetype, Ice.Current __current)
      Register an OriginalFile using its path
      OriginalFile root​(Ice.Current __current)
      Return the OriginalFile descriptor for this Repository.
      java.lang.String rootPath​(org.hibernate.Session session, ome.system.ServiceFactory serviceFactory)  
      void setApplicationContext​(org.springframework.context.ApplicationContext applicationContext)  
      protected java.lang.String stackTraceAsString​(java.lang.Throwable t)  
      protected PublicRepositoryI.AMD_submit submitRequest​(ServiceFactoryI sf, Request req, Ice.Current current)  
      protected PublicRepositoryI.AMD_submit submitRequest​(ServiceFactoryI sf, Request req, Ice.Current current, ome.services.util.Executor.Priority priority)  
      protected Ice.Current sudo​(Ice.Current current, java.lang.String sessionUuid)
      Provide a Current like the given one, except with the request context session UUID replaced.
      Ice.Object tie()
      Wrap the current instance with an TieBase so that it can be turned into a proxy.
      RMap treeList​(java.lang.String path, Ice.Current __current)
      Similar to list but recursive and returns only primitive values for the file at each location.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • DIRECTORY_MIMETYPE

        public static final java.lang.String DIRECTORY_MIMETYPE
        Mimetype used to connote a directory OriginalFile object.
        See Also:
        Constant Field Values

      • IMPORT_LOG_MIMETYPE

        public static final java.lang.String IMPORT_LOG_MIMETYPE
        media type for import logs
        See Also:
        Constant Field Values

      • checksumProviderFactory

        protected final ome.util.checksum.ChecksumProviderFactory checksumProviderFactory

      • checksumAlgorithms

        protected final com.google.common.collect.ImmutableList<ChecksumAlgorithm> checksumAlgorithms

      • context

        protected ome.system.OmeroContext context

    • Constructor Detail

      • PublicRepositoryI

        public PublicRepositoryI​(RepositoryDao repositoryDao,
                         ome.util.checksum.ChecksumProviderFactory checksumProviderFactory,
                         java.lang.String checksumAlgorithmSupported,
                         java.lang.String pathRules)
                  throws ServerError
        Throws:
        ServerError

    • Method Detail

      • initialize

        public void initialize​(FileMaker fileMaker,
                       java.lang.Long id,
                       java.lang.String repoUuid)
                throws ValidationException
        Called by the internal repository once initialization has taken place.
        Parameters:
        fileMaker -
        id -
        Throws:
        ValidationException

      • tie

        public Ice.Object tie()
        Wrap the current instance with an TieBase so that it can be turned into a proxy. This is required due to the subclassing between public repo instances.

      • getRepoUuid

        public java.lang.String getRepoUuid()

      • root

        public OriginalFile root​(Ice.Current __current)
                  throws ServerError
        Description copied from interface: _RepositoryOperations
        Return the OriginalFile descriptor for this Repository. It will have the path of the repository's root on the underlying filesystem.
        Specified by:
        root in interface _RepositoryOperations
        Parameters:
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • fileExists

        public boolean fileExists​(java.lang.String path,
                          Ice.Current __current)
                   throws ServerError
        Description copied from interface: _RepositoryOperations
        Returns true if the file or path exists within the repository. In other words, if a call on `dirname path` to listFiles would return an object for this path.
        Specified by:
        fileExists in interface _RepositoryOperations
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • list

        public java.util.List<java.lang.String> list​(java.lang.String path,
                                             Ice.Current __current)
                                      throws ServerError
        Description copied from interface: _RepositoryOperations
        Returns a set of strings naming the files and directories in the directory denoted by an abstract pathname.
        Specified by:
        list in interface _RepositoryOperations
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • listFiles

        public java.util.List<OriginalFile> listFiles​(java.lang.String path,
                                              Ice.Current __current)
                                       throws ServerError
        Description copied from interface: _RepositoryOperations
        Returns an array of abstract pathname objects denoting the files in the directory denoted by an abstract pathname. It is expected that at a minimum the ""name"", ""path"", ""size"" and ""mtime"" attributes will be present for each OriginalFile instance.
        Specified by:
        listFiles in interface _RepositoryOperations
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • treeList

        public RMap treeList​(java.lang.String path,
                     Ice.Current __current)
              throws ServerError
        Description copied from interface: _RepositoryOperations
        Similar to list but recursive and returns only primitive values for the file at each location. Guaranteed for each path is only the values id and mimetype. After a call to unwrap, the returned RMap for a call to treeList("/user_1/dir0") might look something like: 
         
 {
 "/user_1/dir0/file1.txt" :
 {
 "id":10,
 "mimetype":
 "binary",
 "size": 10000L
 },

 "/user_1/dir0/dir1" :
 {
 "id": 100,
 "mimetype": "Directory",
 "size": 0L,
 "files":
 {
 "/user_1/dir0/dir1/file1indir.txt" :
 {
 "id": 1,
 "mimetype": "png",
 "size": 500
 }
 }
 }
 }
        Specified by:
        treeList in interface _RepositoryOperations
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • rootPath

        public java.lang.String rootPath​(org.hibernate.Session session,
                                 ome.system.ServiceFactory serviceFactory)
                          throws ServerError
        Parameters:
        session - the Hibernate session
        serviceFactory - the service factory
        Returns:
        the filesystem path set for this repository's root directory
        Throws:
        ServerError - if the root path could not be retrieved

      • register

        public OriginalFile register​(java.lang.String path,
                             RString mimetype,
                             Ice.Current __current)
                      throws ServerError
        Register an OriginalFile using its path
        Specified by:
        register in interface _RepositoryOperations
        Parameters:
        path - Absolute path of the file to be registered.
        mimetype - Mimetype as an RString
        __current - ice context.
        Returns:
        The OriginalFile with id set (unloaded)
        Throws:
        ServerError

      • deletePaths

        public HandlePrx deletePaths​(java.lang.String[] files,
                             boolean recursive,
                             boolean force,
                             Ice.Current __current)
                      throws ServerError
        Delete paths recursively as described in Repositories.ice. Internally uses treeList(String, Ice.Current) to build the recursive list of files.
        Specified by:
        deletePaths in interface _RepositoryOperations
        Parameters:
        files - non-null, preferably non-empty list of files to check.
        recursive - See Repositories.ice for an explanation
        force - See Repositories.ice for an explanation
        __current - Non-null ice context.
        Throws:
        ServerError

      • mimetype

        public java.lang.String mimetype​(java.lang.String path,
                                 Ice.Current __current)
                          throws ServerError
        Get the mimetype for a file.
        Specified by:
        mimetype in interface _RepositoryOperations
        Parameters:
        path - A path on a repository.
        __current - ice context.
        Returns:
        mimetype
        Throws:
        ServerError

      • file

        public RawFileStorePrx file​(java.lang.String path,
                            java.lang.String mode,
                            Ice.Current __current)
                     throws ServerError
        Description copied from interface: _RepositoryOperations
        Returns a special RawFileStore which permits only the operations set out in the options string ""wb"", ""a+"", etc. FIXME: Initially only ""r"" and ""rw"" are supported as these are handled directly by RandomAccessFile and so don't break the current implementation. Any call to that tries to break the options will throw an ApiUsageException. If a file exists at the given path, a ValidationException will be thrown.
        Specified by:
        file in interface _RepositoryOperations
        __current - The Current object for the invocation.
        Throws:
        ServerError

      • findInDb

        protected OriginalFile findInDb​(CheckedPath checked,
                                java.lang.String mode,
                                Ice.Current current)
                         throws ServerError
        Find the given path in the DB or create. "requiresWrite" is set to true unless the mode is "r". If requiresWrite is true, then the caller needs the file to be modifiable (both on disk and the DB). If this doesn't hold, then a SecurityViolation will be thrown.
        Throws:
        ServerError

      • persistLogFile

        @Deprecated
protected ome.model.core.OriginalFile persistLogFile​(ome.model.core.OriginalFile originalFile,
                                                     Ice.Current current)
                                              throws ServerError
        Deprecated.
        Set the repository of the given original file to be this one.
        Parameters:
        originalFile - the ID of the log file
        current - the Ice method invocation context
        Throws:
        ServerError

      • makeAdjustedCurrent

        protected Ice.Current makeAdjustedCurrent​(Ice.Current __current)

      • sudo

        protected Ice.Current sudo​(Ice.Current current,
                           java.lang.String sessionUuid)
        Provide a Current like the given one, except with the request context session UUID replaced.
        Parameters:
        current - an Current instance
        sessionUuid - a new session UUID for the instance
        Returns:
        a new Current instance like the given one but with the new session UUID

      • createRepoRFS

        protected RawFileStorePrx createRepoRFS​(CheckedPath checked,
                                        java.lang.String mode,
                                        Ice.Current __current)
                                 throws ServerError,
                                        InternalException
        Create, initialize, and register an RepoRawFileStoreI with the proper setting (read or write).
        Parameters:
        checked - The file that will be read. Can't be null, and must have ID set.
        mode - The mode for writing. If null, read-only.
        __current - The current user's session information.
        Returns:
        A proxy ready to be returned to the user.
        Throws:
        ServerError
        InternalException

      • getFactory

        protected Ice.ObjectFactory getFactory​(java.lang.String id,
                                       Ice.Current current)

      • makeDir

        public void makeDir​(java.lang.String path,
                    boolean parents,
                    Ice.Current current)
             throws ServerError
        Create a nested path in the repository. Creates each directory in the path is it doen't already exist. Silently returns if the directory already exists.
        Specified by:
        makeDir in interface _RepositoryOperations
        Parameters:
        path - A path on a repository.
        parents - Boolean switch like the "mkdir -p" flag in unix.
        current - ice context.
        Throws:
        ServerError

      • makeDir

        public void makeDir​(CheckedPath checked,
                    boolean parents,
                    org.hibernate.Session s,
                    ome.system.ServiceFactory sf,
                    ome.util.SqlAction sql,
                    ome.system.EventContext effectiveEventContext)
             throws ServerError
        Throws:
        ServerError

      • makeCheckedDirs

        protected void makeCheckedDirs​(java.util.LinkedList<CheckedPath> paths,
                               boolean parents,
                               org.hibernate.Session s,
                               ome.system.ServiceFactory sf,
                               ome.util.SqlAction sql,
                               ome.system.EventContext effectiveEventContext)
                        throws ServerError
        Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
        Parameters:
        paths - Not null, not empty. (Will be emptied by this method.)
        parents - "mkdir -p" like flag.
        s - the Hibernate session
        sf - the service factory
        sql - the JDBC convenience wrapper
        effectiveEventContext - the event context to apply
        Throws:
        ServerError

      • makeCheckedDirs

        protected void makeCheckedDirs​(java.util.LinkedList<CheckedPath> paths,
                               boolean parents,
                               org.hibernate.Session s,
                               ome.system.ServiceFactory sf,
                               ome.util.SqlAction sql,
                               ome.system.EventContext effectiveEventContext,
                               java.util.function.Consumer<CheckedPath> fileCreationListener)
                        throws ServerError
        Internal method to be used by subclasses to perform any extra checks on the listed of CheckedPath instances before allowing the creation of directories.
        Parameters:
        paths - Not null, not empty. (Will be emptied by this method.)
        parents - "mkdir -p" like flag.
        s - the Hibernate session
        sf - the service factory
        sql - the JDBC convenience wrapper
        effectiveEventContext - the event context to apply
        fileCreationListener - the file creation listener to notify of new directories being created
        Throws:
        ServerError

      • setApplicationContext

        public void setApplicationContext​(org.springframework.context.ApplicationContext applicationContext)
                           throws org.springframework.beans.BeansException
        Specified by:
        setApplicationContext in interface org.springframework.context.ApplicationContextAware
        Throws:
        org.springframework.beans.BeansException

      • stackTraceAsString

        protected java.lang.String stackTraceAsString​(java.lang.Throwable t)