--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/workflow/link_to_galaxy.py	Fri Mar 10 16:02:04 2023 +0000
@@ -0,0 +1,116 @@
+#!/usr/bin/env python3
+
+import logging
+logger = logging.getLogger(__name__)
+
+from bioblend.galaxy import GalaxyInstance
+from nexusformat.nexus import *
+from os import path
+from yaml import safe_load
+
+from .models import import_scanparser, TomoWorkflow
+
+def get_folder_id(gi, path):
+    library_id = None
+    folder_id = None
+    folder_names = path[1:] if len(path) > 1 else []
+    new_folders = folder_names
+    libs = gi.libraries.get_libraries(name=path[0])
+    if libs:
+        for lib in libs:
+            library_id = lib['id']
+            folders = gi.libraries.get_folders(library_id, folder_id=None, name=None)
+            for i, folder in enumerate(folders):
+                fid = folder['id']
+                details = gi.libraries.show_folder(library_id, fid)
+                library_path = details['library_path']
+                if library_path == folder_names:
+                    return (library_id, fid, [])
+                elif len(library_path) < len(folder_names):
+                    if library_path == folder_names[:len(library_path)]:
+                        nf = folder_names[len(library_path):]
+                        if len(nf) < len(new_folders):
+                            folder_id = fid
+                            new_folders = nf
+    return (library_id, folder_id, new_folders)
+
+def link_to_galaxy(filename:str, galaxy=None, user=None, password=None, api_key=None) -> None:
+    # Read input file
+    extension = path.splitext(filename)[1]
+    if extension == '.yml' or extension == '.yaml':
+        with open(filename, 'r') as f:
+            data = safe_load(f)
+    elif extension == '.nxs':
+        with NXFile(filename, mode='r') as nxfile:
+            data = nxfile.readfile()
+    else:
+        raise ValueError(f'Invalid filename extension ({extension})')
+    if isinstance(data, dict):
+        # Create Nexus format object from input dictionary
+        wf = TomoWorkflow(**data)
+        if len(wf.sample_maps) > 1:
+            raise ValueError(f'Multiple sample maps not yet implemented')
+        nxroot = NXroot()
+        for sample_map in wf.sample_maps:
+            import_scanparser(sample_map.station)
+            sample_map.construct_nxentry(nxroot, include_raw_data=False)
+        nxentry = nxroot[nxroot.attrs['default']]
+    elif isinstance(data, NXroot):
+        nxentry = data[data.attrs['default']]
+    else:
+        raise ValueError(f'Invalid input file data ({data})')
+
+    # Get a Galaxy instance
+    if user is not None and password is not None :
+        gi = GalaxyInstance(url=galaxy, email=user, password=password)
+    elif api_key is not None:
+        gi = GalaxyInstance(url=galaxy, key=api_key)
+    else:
+        exit('Please specify either a valid Galaxy username/password or an API key.')
+
+    cycle = nxentry.instrument.source.attrs['cycle']
+    btr = nxentry.instrument.source.attrs['btr']
+    sample = nxentry.sample.name
+
+    # Create a Galaxy work library/folder
+    # Combine the cycle, BTR and sample name as the base library name
+    lib_path = [p.strip() for p in f'{cycle}/{btr}/{sample}'.split('/')]
+    (library_id, folder_id, folder_names) = get_folder_id(gi, lib_path)
+    if not library_id:
+        library = gi.libraries.create_library(lib_path[0], description=None, synopsis=None)
+        library_id = library['id']
+#        if user:
+#            gi.libraries.set_library_permissions(library_id, access_ids=user,
+#                    manage_ids=user, modify_ids=user)
+        logger.info(f'Created Library:\n{library}')
+    if len(folder_names):
+        folder = gi.libraries.create_folder(library_id, folder_names[0], description=None,
+                base_folder_id=folder_id)[0]
+        folder_id = folder['id']
+        logger.info(f'Created Folder:\n{folder}')
+        folder_names.pop(0)
+        while len(folder_names):
+            folder = gi.folders.create_folder(folder['id'], folder_names[0],
+                    description=None)
+            folder_id = folder['id']
+            logger.info(f'Created Folder:\n{folder}')
+            folder_names.pop(0)
+
+    # Create a sym link for the Nexus file
+    dataset = gi.libraries.upload_from_galaxy_filesystem(library_id, path.abspath(filename),
+            folder_id=folder_id, file_type='auto', dbkey='?', link_data_only='link_to_files',
+            roles='', preserve_dirs=False, tag_using_filenames=False, tags=None)[0]
+
+    # Make a history for the data
+    history_name = f'tomo {btr} {sample}'
+    history = gi.histories.create_history(name=history_name)
+    logger.info(f'Created history:\n{history}')
+    history_id = history['id']
+    gi.histories.copy_dataset(history_id, dataset['id'], source='library')
+
+# TODO add option to either 
+#     get a URL to share the history
+#     or to share with specific users
+# This might require using: 
+#     https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/docs.html#using-bioblend-for-raw-api-calls
+