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GalaxyLibraryContents Class Reference

Public Member Functions

 __construct (GalaxyInstance $galaxy)
 
 index ($params)
 
 show ($params)
 
 create ($params)
 

Constructor & Destructor Documentation

GalaxyLibraryContents::__construct ( GalaxyInstance  $galaxy)

The Folders constructor.

Parameters
GalaxyInstance$galaxyA GalaxyInstance object.
Returns
An instance of a Libraries object.

Member Function Documentation

GalaxyLibraryContents::create (   $params)

Add a folder/file/data collection to the specified the library.

This is one is important when you want to upload files to said library from a local filesystem to the given galaxy instance.

POST /api/libraries/{library_id}/contents To copy an HDA into a library send 'create_type' of 'file' and the HDA's encoded id in from 'from_hda_id' (and optionally 'ldda_message').

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • library_id: The repository where you want to 'create' this new data.
  • folder_id: A folder within a library to 'create' this new data.
  • create_type: The type of data category - file, folder, or collection.
  • collection_type (Only if create_type is 'collection'): Can be list, paired, list:paired.
  • element_identifiers (Only if create_type is 'collection'): List defining collection (the actual data for this new collection).
  • from_hda_id (Only if create_type is file): Id of HDA to copy into The library.
  • ldda_message (Optional): The new message attribute of the LDDA created.
  • extended_metadata (Optional): Sub-dictionary containing metadata to associate with the item.
  • upload_option (Optional): When POST'ed to the url, the default value is 'upload_file'. Other options include 'upload_directory' or 'upload_paths'.
  • server_dir (Only if upload_option is 'upload_directory'): Relative path of the subdirectory of Galaxy 'library_import_dir' (look for in galaxy.ini) to upload. All and only the files (no subdirectories) contained in the specified directory will be uploaded.
  • filesystem_paths (Only if upload_option is 'upload_paths' AND if user is an admin): File paths on the Galaxy server to upload to the library one file per line.
  • link_data_only (Only when upload_option is 'upload_directory' or 'upload_paths'): Either 'copy_files' which is default, or 'link_to_files'. Setting to 'link_to_files' symlinks instead of copying the files.
  • name (Only if create_type is 'folder'): Name of the folder to create.
  • description (Only if create_type is 'folder'): Description of folder.
Returns
The data that was uploaded and its metadata.
GalaxyLibraryContents::index (   $params)

Gather the contents from the specified libarary. GET /api/libraries/{encoded_library_id}

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • library_id: Unique id of a library to view its contents.
Returns
Files and Folders within the specified library.
GalaxyLibraryContents::show (   $params)

View the specified library content within a given library.

GET /api/libraries/{encoded_library_id}/

You need both of the specific id's in order to see the information of the content.

Parameters
$paramsAn associative array containing the input parameters for this function. The following parameters are available:
  • library_id: Unique id of a libary to view a specified content.
  • library_content_id: An entry within the library that contains data.
Returns
Detailed library item information.
The documentation for this class was generated from the following file: