public
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#
__construct( string $name )
Fileserver constructor.
Parameters
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public
boolean
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isReachable( )
Checks whether the file area is reachable.
Checks whether the file area is reachable.
Returns
boolean True if the file area is reachable (i.e. if source
and destination folders exist).
Todo
Test if accessible/writable.
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public
string
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username( )
Returns the name of the user.
Returns the name of the user.
Returns
string Name of the user.
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public
string
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sourceFolder( )
Returns the absolute path to the user's source image folder. The folder may be on the local network.
Returns the absolute path to the user's source image folder. The folder may be on the local network.
Returns
string Absolute path to the source image folder.
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public
string
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destinationFolder( )
Returns the absolute path to the user's destination image folder. The folder may be on the local network
Returns the absolute path to the user's destination image folder. The folder may be on the local network
Returns
string Absolute path to the destination image folder.
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public
string
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destinationFolderFor( hrm\job\JobDescription $desc )
Returns the destination image folder from a JobDescription object
Returns the destination image folder from a JobDescription object
Parameters
- $desc
- JobDescription object.@
Returns
string Festination image folder with user-generated subfolder.
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public
array|boolean
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#
files( string $extension = null )
Searches the source folder recursively, stores and also returns the list of found files
Searches the source folder recursively, stores and also returns the list of found files
Parameters
- $extension
- Extension to be considered to scan the folder. Omit to get all files.
Returns
array|boolean Sorted array of file names or false if the source folder does not exist.
Todo
Do not return different types!
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public
string
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checkAgainstFormat( string $file, string $selectedFormat )
Extracts the file extension, also if it's a subimage.
Extracts the file extension, also if it's a subimage.
Parameters
- $file
- The file name.
- $selectedFormat
- The format selected at the select images stage.
Returns
string The file extension.
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public
array
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listFiles( boolean $expand )
Searches the source folder recursively and returns all found files
Searches the source folder recursively and returns all found files
Parameters
- $expand
If true, names of subimages (as in the case of
lif files) are expanded and returned in the list of file names.
Please notice that this function DOES NOT STORE THE LIST OF FILES. It
just returns it!
Returns
array Sorted array of file names.
Todo
Refactor!
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public
array|boolean
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destFiles( string $extension = null )
Searches the destination folder recursively and returns all found files.
Searches the destination folder recursively and returns all found files.
Parameters
- $extension
- Extension to be considered to scan the folder. Omit to get all files.
Returns
array|boolean Sorted array of file names or false if the destination folder does not exist.
Todo
Do not return different types!
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public
array
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condenseSeries( )
Condense file series by preserving only the first file of each series.
Condense file series by preserving only the first file of each series.
Files that do not belong to a series are preserved.
Returns
array Updated (condensed) list of stored files.
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public
boolean
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isPartOfFileSeries( string $file )
Checks whether a given file belongs to a file series.
Checks whether a given file belongs to a file series.
Parameters
- $file
- The file to be checked.
Returns
boolean True if the file belongs to a series, false otherwise.
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public
array
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filesOfType( string $format, boolean $isTimeSeries )
A wrapper function to list files of a certain type.
A wrapper function to list files of a certain type.
This updates the list of stored files.
Parameters
- $format
- Extension to be considered to scan the folder.
- $isTimeSeries
- True for time series, false otherwise.
Returns
array Array of of file names.
Todo
Refactor!
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public
array
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allFiles( )
Scans the image source folder recursively and returns all files.
Scans the image source folder recursively and returns all files.
This does not update the stored list!
Returns
array Sorted array of file names
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public
array
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#
tiffFiles( )
Convenience method to get TIFF files.
Convenience method to get TIFF files.
This stores the files.
Returns
array Array of TIFF file names.
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public
array
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tiffSeriesFiles( )
Convenience method to get numbered TIFF series.
Convenience method to get numbered TIFF series.
This stores the files.
Returns
array Array of numbered TIFF file names.
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public
array
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#
tiffLeicaFiles( )
Convenience method to get TIFF series with Leica style numbering
Convenience method to get TIFF series with Leica style numbering
This stores the files.
Returns
array Array of Leica TIFF file names.
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public
array
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stkFiles( )
Convenience method to get all STK files (also unprocessed time series).
Convenience method to get all STK files (also unprocessed time series).
This stores the files.
Returns
array Array of STK files with unprocessed time series.
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public
array
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stkSeriesFiles( )
Convenience method to get STK time series files (*_t#.stk).
Convenience method to get STK time series files (*_t#.stk).
This stores the files.
Returns
array Array of STK time series files.
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public
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resetFiles( )
Resets the list of source files. Next time the list is accessed
it will be recreated automatically.
Resets the list of source files. Next time the list is accessed
it will be recreated automatically.
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public
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#
resetDestFiles( )
Resets the list of destination files. Next time the list is accessed
it will be recreated automatically.
Resets the list of destination files. Next time the list is accessed
it will be recreated automatically.
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public
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expandSubImages( boolean $bool )
Sets a flag to indicate whether multi-experiment image files should
be expanded in file lists or not.
Sets a flag to indicate whether multi-experiment image files should
be expanded in file lists or not.
Parameters
- $bool
- True if multi-image files should be expanded; false otherwise.
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public
array
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selectedFiles( )
Returns the list of selected files that will be added to a job.
Returns the list of selected files that will be added to a job.
Returns
array Array of selected file names.
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public
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addFilesToSelection( array $files )
Add files to current selection if they are not already contained.
Add files to current selection if they are not already contained.
Parameters
- $files
- Array of file names to be added.
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public
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removeAllFilesFromSelection( )
Remove all files from current selection.
Remove all files from current selection.
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public
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removeFilesFromSelection( array $files )
Remove files from current selection (if they are in).
Remove files from current selection (if they are in).
Parameters
- $files
- Array of file names to be removed,
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public
string
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getFilePattern( string $fileName )
Builds a regular expression to be able to look for files based on the job id.
Builds a regular expression to be able to look for files based on the job id.
Parameters
- $fileName
- File name to be parsed to construct the regular expression.
Returns
string The regular expression.
Todo
A new design and implementation of the file server is necessary.
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public
string
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downloadResults( array $files )
Packs a series of files to download.
Packs a series of files to download.
Parameters
- $files
- List of files to be added.
Returns
string Success/error message.
Todo
This will be replaced soon!
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public
string
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deleteFiles( array $files, string $dir = "dest" )
Deletes a list of files and all dependent sub-files (e.g. thumbnails and so)
from a user directory.
Deletes a list of files and all dependent sub-files (e.g. thumbnails and so)
from a user directory.
Parameters
- $files
- Array of image file names.
- $dir
- Folder to consider, one of 'src' or 'dest'
Returns
string Error message in case files could not be deleted.
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public
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#
exportToOmero( )
Exports a deconvolved image to the OMERO server.
Exports a deconvolved image to the OMERO server.
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public
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#
importFromOmero( )
Imports a raw image from the OMERO server.
Imports a raw image from the OMERO server.
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public
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decompressArchive( string $file, string $type, string $dest, &string & $okMsg, &string & $errMsg, string $subdir = "", boolean $imagesOnly = true )
Extracts files from compressed archives.
Extracts files from compressed archives.
Parameters
- $file
- Archive name.
- $type
- Archive type (zip, tar, tgz...).
- $dest
- Destination path.
- $okMsg
- A reference to a string to accumulate OK messages.
- $errMsg
- A reference to a string to accumulate error messages.
- $subdir
An optional subdirectory under $dest to expand the
files to.
- $imagesOnly
An optional flag to delete non-image files after
extraction.
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public
string
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uploadFiles( array $files, string $dir )
Processes the $_FILES array posted when uploading files, moving
valid one to the specified directory. Compressed files are
decompressed.
Processes the $_FILES array posted when uploading files, moving
valid one to the specified directory. Compressed files are
decompressed.
Parameters
- $files
- Array of files to be uploaded.
- $dir
- Destination path, one of 'src' or 'dest'.
Returns
string Message with details.
See
See PHP documentation: POST method uploads.
Todo
This will be replaced soon!
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public
array
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#
imageExtensions( )
Returns a list of file extensions for supported images
Returns a list of file extensions for supported images
Returns
array Array of file extensions.
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public
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#
setImageExtensions( array $extensions )
Sets the list of image extensions.
Sets the list of image extensions.
Files with these extensions under the user's source folder will be
shown under available images. Whenever the image extensions are changed,
the files and the selected files will be reset. Only exception is when
the list of image extensions is replaced by itself.
Parameters
- $extensions
- Array of file extensions (strings)
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public
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setDefaultImageExtensions( )
Sets the image extensions from the list of valid image extensions.
Sets the image extensions from the list of valid image extensions.
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public
boolean
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isImage( string $filename )
Checks whether the filename extension matches the currently selected file format.
Checks whether the filename extension matches the currently selected file format.
Parameters
- $filename
- File name to be checked.
Returns
boolean True if the file extension matches the file format, false otherwise.
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public
boolean
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isValidImage( string $filename, boolean $alsoExtras = false )
Checks whether the file name is of a valid type.
Checks whether the file name is of a valid type.
Parameters
- $filename
- The file name to be checked.
- $alsoExtras
- If true, consider also extensions as ids or ids.gz.
Returns
boolean True if the filename is of a valid type, false otherwise.
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public
string
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getCompressedArchiveType( string $filename )
Returns the archive type of a filename, if it is a valid known compressed archive.
Returns the archive type of a filename, if it is a valid known compressed archive.
Parameters
- $filename
- The file name to be checked.
Returns
string The archive type if the filename is valid archive, "" otherwise.
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public
string
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getValidArchiveTypesAsString( )
Returns all archive types as string.
Returns all archive types as string.
Returns
string String containing all archive types.
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public
array
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#
getSubImages( array $files )
When the selected file type is one that can contain sub-images
(like LIF), the already built list of $this->files is extended to
show all the available sub-images. This is done by querying HuCore.
When the selected file type is one that can contain sub-images
(like LIF), the already built list of $this->files is extended to
show all the available sub-images. This is done by querying HuCore.
Parameters
- $files
- Array of file names that have to be inspected for sub-images.
Returns
array Updated array of file names with sub-images.
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public
array
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getMetaDataFromFiles( array $files )
Some files like ICS can report their metadata without having to
open the whole image, which is good e.g. to see the compatibility
of the selected PSF with the current Parameter Setting.
This is done by querying HuCore.
Some files like ICS can report their metadata without having to
open the whole image, which is good e.g. to see the compatibility
of the selected PSF with the current Parameter Setting.
This is done by querying HuCore.
Parameters
- $files
- Array of file paths (relative to the source folder).
Returns
array N-dimensional array of metadata per file.
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public
array
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getMetaData( string $type = "ics", string $file = "all" )
Some files like ICS can report their metadata without having to
open the whole image, which is good e.g. to see the compatibility
of the selected PSF with the current Parameter Setting.
This is done by querying HuCore.
Some files like ICS can report their metadata without having to
open the whole image, which is good e.g. to see the compatibility
of the selected PSF with the current Parameter Setting.
This is done by querying HuCore.
Parameters
- $type
- File type, default is "ics".
- $file
This can be a file name for the file to be inspected, or
"all" to inspect all the files of type $type that are in the source folder.
Returns
array N-dimensional array of metadata per file.
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public
string
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getImageOptionLine( string $file, integer $index, string $dir, string $type, integer $ref = 0, integer $data = 1 )
Generates a html line for a form listing images in the server
Generates a html line for a form listing images in the server
Parameters
- $file
- Image file name.
- $index
- Unused Index in the file name array.
- $dir
- Unused Destination directory, one of 'src', or 'dst'.
- $type
- Unused Type of the image, e.g. 'preview'.
- $ref
- Unused Default is 0.
- $data
- Unused Default = 1.
Returns
string The html code for the form.
Todo
Check why this function taks 6 parameters and uses only one.
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public
string
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getImageAction( string $file, integer $index, string $dir, string $type, integer $ref = 0, integer $data = 1 )
Generates a javascript command to show an image preview.
Generates a javascript command to show an image preview.
Parameters
- $file
- Image file name.
- $index
- Index in the file name array.
- $dir
- Destination directory, one of 'src', or 'dst'.
- $type
- Type of the image, e.g. 'preview'.
- $ref
- Default is 0.
- $data
- Default = 1.
Returns
string The javascript code.
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public
string
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imgPreview( string $image, string $dir, string $type = "preview_xy", boolean $escape = true )
Generates a link to retrieve an image thumbnail, which is a jpg file saved near the file itself.
Generates a link to retrieve an image thumbnail, which is a jpg file saved near the file itself.
Parameters
- $image
- Image file name.
- $dir
- Destination directory, one of 'src' or 'dst'.
- $type
Type of thumbnail, one of 'preview_xy', 'preview_xz',
'preview_yz'; default is 'preview_xy'.
- $escape
- If true, the code is escaped to be used in Javascript code.
Returns
string An link to securely get the thumbnail.
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public
string
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viewStrip( string $file, string $type = "stack.compare", string $dir = "dest", boolean $frame = false, integer $margin = 25 )
Shows stacks and time series saved as jpeg strips in a css container.
Inspired by the paperbird code by Rom�n Cort�s:
Shows stacks and time series saved as jpeg strips in a css container.
Inspired by the paperbird code by Rom�n Cort�s:
Parameters
- $file
- Image file name.
- $type
Type of the strip, one of 'stack.compare', 'tSeries.compare',
'preview_yz'; default is 'stack.compare'.
- $dir
- Destination directory, one of 'src' or 'dest', default is 'dest'.
- $frame
- True to draw a frame, false otherwise.
- $margin
- Thickness of the margin around th strip, default is 25.
Returns
string HTML code to be output to the page.
See
http://www.romancortes.com/blog/css-paper-bird/
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public
string
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previewPage( string $file, string $op = "close", string $mode = "MIP", integer $size = 400 )
Creates the preview page for the file browser.
Creates the preview page for the file browser.
Parameters
- $file
- Image file name.
- $op
- Operation, one of 'close' or 'home'. Default is "close".
- $mode
Display mode. One of "MIP", "parameters", "log", "SFP", "stack", "tSeries",
"history", "remarks". Default is "MIP".
- $size
- Size of the thumbnail. Default is 400.
Returns
string HTML code (whole page).
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public
string
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compareResult( string $file, integer|string $size = "400", string $op = "close", string $mode = "MIP" )
Shows original/result previews side by side.
Shows original/result previews side by side.
Parameters
- $file
- Image file name.
- $size
- Size of the thumbnail. Default is 400
- $op
- Operation, one of 'close' or 'home'. Default is "close".
- $mode
Display mode. One of "MIP, "SFP", "stack", "tSeries", "log",
"history", "remarks". Default is "MIP".
Returns
string HTML code (whole page).
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public
string
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genPreview( string $file, string $src, string $dest, integer $index, integer|string $sizes = "preview", string|integer $data = 0 )
Calls hucore to open an image and generate a jpeg preview.
Calls hucore to open an image and generate a jpeg preview.
Parameters
- $file
- Image file name.
- $src
- Directory, one of 'src' or 'dest'.
- $dest
- Directory, one of 'src' or 'dest'.
- $index
- Index.
- $sizes
- Either an integer, or "preview". Default = "preview".
- $data
- Either some data (unclear) or 0. Default = 0.
Returns
string HTML page (complete).
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public
string
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getThumbnail( string $file, string $dir )
Serves a certain file from the dest directory. Intended to serve
jpg thumbails in combination with imgThumbnail.
Serves a certain file from the dest directory. Intended to serve
jpg thumbails in combination with imgThumbnail.
Parameters
- $file
- Image file name.
- $dir
- Directory, either 'src' or 'dest'.
Returns
string Served binary file.
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public
string
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getMovie( string $file, string $dir = "dest" )
Serves an existing AVI movie.
Serves an existing AVI movie.
Parameters
- $file
- Image file name.
- $dir
- Directory, either 'src' or 'dest'. Default is 'dest'.
Returns
string Served binary file.
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public
boolean
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hasSelection( )
Returns true if at least one file is selected.
Returns true if at least one file is selected.
Returns
boolean True if at least one file is selected.
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public
boolean
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folderContains( string $folder, string $filename )
Checks if a folder contains a given file name.
Checks if a folder contains a given file name.
Parameters
- $folder
- Folder name
- $filename
- File name.
Returns
boolean True if the folder contains the file name.
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public
boolean
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folderContainsNewerFile( string $folder, string $date )
Checks if a folder contains newer files than a given date.
Checks if a folder contains newer files than a given date.
Parameters
- $folder
- Directory to be checked.
- $date
- Date string.
Returns
boolean True if at least one file is more recent than date.
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public
array
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#
createHardLinksToSharedPSFs( array $psfFiles, string $targetUser )
Create hard links into the psf_sharing/buffer folder from the
folder of the sharing user and return an array of full paths
created links.
Create hard links into the psf_sharing/buffer folder from the
folder of the sharing user and return an array of full paths
created links.
Parameters
- $psfFiles
- Array of psf files paths relatives to current user.
- $targetUser
- name of the target user.
Returns
array Array of destination PSF paths.
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public
array
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#
createHardLinksFromSharedPSFs( array $psfFiles, string $targetUser, string $previousUser )
Create hard links into the folder of the target user from
the psf_sharing/buffer folder and return an array of full paths
created links.
Create hard links into the folder of the target user from
the psf_sharing/buffer folder and return an array of full paths
created links.
Parameters
- $psfFiles
- array of psf files paths relatives to current user.
- $targetUser
- Name of the target user.
- $previousUser
- Name of the previous (source) user.
Returns
array Array of destination PSF paths.
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public static
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#
deleteSharedFSPFilesFromBuffer( array $psfFiles )
Delete PSF files (hard links) with given relative path from
the psf_sharing/buffer folder.
Delete PSF files (hard links) with given relative path from
the psf_sharing/buffer folder.
Parameters
- $psfFiles
- Array of PSF files paths relative to the file server root.
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public static
string|null
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#
findCompanionFile( string $file )
Given the name of either an ics or and ids file, returns the name of the companion.
Given the name of either an ics or and ids file, returns the name of the companion.
The companion file must exist.
Parameters
- $file
File name with either .ics or .ids extension. The case might
be different (e.g. .ICS).
Returns
string|null Full fine name of the companion file, if it exist; NULL otherwise.
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public
array
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#
getPSFiles( )
Return all files with extension ".ics" and ".h5" found by recursive scan of the source folder.
Return all files with extension ".ics" and ".h5" found by recursive scan of the source folder.
Returns
array Array of file names.
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public static
boolean|null
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#
is_dir_empty( string $dir )
Check if a directory is empty.
Check if a directory is empty.
Parameters
- $dir
- Full path to directory to check.
Returns
boolean|null True if the directory is empty, False if it is not; False
if it is not readable or does not exist.
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