galaxy/doc/source/api/quickstart.rst

Quickstart
==========

Log in as your user, navigate to the API Keys page in the User menu, and
generate a new API key.  Make a note of the API key, and then pull up a
terminal.  Now we'll use the display.py script in your galaxy/scripts/api
directory for a short example, which assumes your local galaxy server is
running on the default port 8080::

        % ./display.py my_key http://localhost:8080/api/histories
        Collection Members
        ------------------
        #1: /api/histories/8c49be448cfe29bc
          name: Unnamed history
          id: 8c49be448cfe29bc
        #2: /api/histories/33b43b4e7093c91f
          name: output test
          id: 33b43b4e7093c91f

The result is a Collection of the histories of the user specified by the API
key (you).  To look at the details of a particular history, say #1 above, do
the following::

        % ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc
        Member Information
        ------------------
        state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0}
        state: ok
        contents_url: /api/histories/8c49be448cfe29bc/contents
        id: 8c49be448cfe29bc
        name: Unnamed history

This gives detailed information about the specific member in question, in this
case the History.  To view history contents, do the following::


        % ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc/contents
        Collection Members
        ------------------
        #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
          name: Pasted Entry
          type: file
          id: 6f91353f3eb0fa4a

What we have here is another Collection of items containing all of the datasets
in this particular history.  Finally, to view details of a particular dataset
in this collection, execute the following::

        % ./display.py my_key http://localhost:8080/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a
        Member Information
        ------------------
        misc_blurb: 1 line
        name: Pasted Entry
        data_type: txt
        deleted: False
        file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat
        state: ok
        download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt
        visible: True
        genome_build: ?
        model_class: HistoryDatasetAssociation
        file_size: 17
        metadata_data_lines: 1
        id: 6f91353f3eb0fa4a
        misc_info: uploaded txt file
        metadata_dbkey: ?

And now you've successfully used the API to request and select a history,
browse the contents of that history, and then look at detailed information
about a particular dataset.

For a more comprehensive Data Library example, set the following option in your
galaxy.ini as well, and restart galaxy again::

        admin_users = you@example.org
        library_import_dir = /path/to/some/directory

In the directory you specified for 'library_import_dir', create some
subdirectories, and put (or symlink) files to import into Galaxy into those
subdirectories.

In Galaxy, create an account that matches the address you put in 'admin_users',
then browse to that user's preferences and generate a new API Key.  Copy the
key to your clipboard and then use these scripts::

        % ./display.py my_key http://localhost:8080/api/libraries
        Collection Members
        ------------------

        0 elements in collection

        % ./library_create_library.py my_key http://localhost:8080/api/libraries api_test 'API Test Library'
        Response
        --------
        /api/libraries/f3f73e481f432006
          name: api_test
          id: f3f73e481f432006

        % ./display.py my_key http://localhost:8080/api/libraries
        Collection Members
        ------------------
        /api/libraries/f3f73e481f432006
          name: api_test
          id: f3f73e481f432006

        % ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006
        Member Information
        ------------------
        synopsis: None
        contents_url: /api/libraries/f3f73e481f432006/contents
        description: API Test Library
        name: api_test

        % ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents
        Collection Members
        ------------------
        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
          name: /
          type: folder
          id: 28202595c0d2591f61ddda595d2c3670

        % ./library_create_folder.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1'
        Response
        --------
        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
          name: api_test_folder1
          id: 28202595c0d2591fa4f9089d2303fd89

        % ./library_upload_from_import_dir.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19
        Response
        --------
        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
          name: 2.bed
          id: e9ef7fdb2db87d7b
        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
          name: 3.bed
          id: 3b7f6a31f80a5018

        % ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents 
        Collection Members
        ------------------
        /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670
          name: /
          type: folder
          id: 28202595c0d2591f61ddda595d2c3670
        /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89
          name: /api_test_folder1
          type: folder
          id: 28202595c0d2591fa4f9089d2303fd89
        /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
          name: /api_test_folder1/2.bed
          type: file
          id: e9ef7fdb2db87d7b
        /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018
          name: /api_test_folder1/3.bed
          type: file
          id: 3b7f6a31f80a5018

        % ./display.py my_key http://localhost:8080/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b
        Member Information
        ------------------
        misc_blurb: 68 regions
        metadata_endCol: 3
        data_type: bed
        metadata_columns: 6
        metadata_nameCol: 4
        uploaded_by: nate@...
        metadata_strandCol: 6
        name: 2.bed
        genome_build: hg19
        metadata_comment_lines: None
        metadata_startCol: 2
        metadata_chromCol: 1
        file_size: 4272
        metadata_data_lines: 68
        message:
        metadata_dbkey: hg19
        misc_info: uploaded bed file
        date_uploaded: 2010-06-22T17:01:51.266119
        metadata_column_types: str, int, int, str, int, str

Other parameters are valid when uploading, they are the same parameters as are
used in the web form, like 'link_data_only' and etc.

The request and response format should be considered alpha and are subject to change.