Hello Ryan,

for interacting with libraries through the Bioblend:

http://bioblend.readthedocs.org/en/latest/api_docs/galaxy/all.html#module-bioblend.galaxy.libraries

for loading data to libraries form the Galaxy's system (e.g. after FTP upload, or when admin):

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/lda_datasets.py#L401

for uploading new files or importing from HDA:

https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/library_contents.py#L144

Hope this helps.

M.

On Fri, Jun 26, 2015 at 12:56 PM Ryan G <ngsbioinformatics@gmail.com> wrote:

By browsing the api code, I discovered library_contents.py that looks like it should be used.  Why this and not folder_contents.py?  There seems to be overlap of these two.  I would expect to upload files to folders within libraries...

On Thu, Jun 25, 2015 at 2:43 PM, Ryan G <ngsbioinformatics@gmail.com> wrote:

Hi all - I'm trying to figure out how to script the ability to upload data (fastq) files to Galaxy via the API.

I can get the Library's root_folder_id, but am unsure of what the API call is to upload a file.  I'm constructing this dictionary:

    data = {}
    data['folder_id'] = galaxyFolderId
    data['create_type'] = 'file'
    data['file_type'] = 'fastq'
    data['upload_option'] = 'upload_paths'
    data['filesystem_paths'] = fileToUpload
    data['link_data_only'] = 'link_to_files'

I assume this is the correct format based on other code I've seen, but I'm not sure what the actual submit call should be. 'api/libraries/' or 'api/folders'????

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/