Mercurial > repos > rv43 > tomo

comparison workflow/link_to_galaxy.py @ 69:fba792d5f83b draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
author rv43
date Fri, 10 Mar 2023 16:02:04 +0000
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children 1cf15b61cd83
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68:ba5866d0251d 69:fba792d5f83b
1 #!/usr/bin/env python3
2
3 import logging
4 logger = logging.getLogger(__name__)
5
6 from bioblend.galaxy import GalaxyInstance
7 from nexusformat.nexus import *
8 from os import path
9 from yaml import safe_load
10
11 from .models import import_scanparser, TomoWorkflow
12
13 def get_folder_id(gi, path):
14 library_id = None
15 folder_id = None
16 folder_names = path[1:] if len(path) > 1 else []
17 new_folders = folder_names
18 libs = gi.libraries.get_libraries(name=path[0])
19 if libs:
20 for lib in libs:
21 library_id = lib['id']
22 folders = gi.libraries.get_folders(library_id, folder_id=None, name=None)
23 for i, folder in enumerate(folders):
24 fid = folder['id']
25 details = gi.libraries.show_folder(library_id, fid)
26 library_path = details['library_path']
27 if library_path == folder_names:
28 return (library_id, fid, [])
29 elif len(library_path) < len(folder_names):
30 if library_path == folder_names[:len(library_path)]:
31 nf = folder_names[len(library_path):]
32 if len(nf) < len(new_folders):
33 folder_id = fid
34 new_folders = nf
35 return (library_id, folder_id, new_folders)
36
37 def link_to_galaxy(filename:str, galaxy=None, user=None, password=None, api_key=None) -> None:
38 # Read input file
39 extension = path.splitext(filename)[1]
40 if extension == '.yml' or extension == '.yaml':
41 with open(filename, 'r') as f:
42 data = safe_load(f)
43 elif extension == '.nxs':
44 with NXFile(filename, mode='r') as nxfile:
45 data = nxfile.readfile()
46 else:
47 raise ValueError(f'Invalid filename extension ({extension})')
48 if isinstance(data, dict):
49 # Create Nexus format object from input dictionary
50 wf = TomoWorkflow(**data)
51 if len(wf.sample_maps) > 1:
52 raise ValueError(f'Multiple sample maps not yet implemented')
53 nxroot = NXroot()
54 for sample_map in wf.sample_maps:
55 import_scanparser(sample_map.station)
56 sample_map.construct_nxentry(nxroot, include_raw_data=False)
57 nxentry = nxroot[nxroot.attrs['default']]
58 elif isinstance(data, NXroot):
59 nxentry = data[data.attrs['default']]
60 else:
61 raise ValueError(f'Invalid input file data ({data})')
62
63 # Get a Galaxy instance
64 if user is not None and password is not None :
65 gi = GalaxyInstance(url=galaxy, email=user, password=password)
66 elif api_key is not None:
67 gi = GalaxyInstance(url=galaxy, key=api_key)
68 else:
69 exit('Please specify either a valid Galaxy username/password or an API key.')
70
71 cycle = nxentry.instrument.source.attrs['cycle']
72 btr = nxentry.instrument.source.attrs['btr']
73 sample = nxentry.sample.name
74
75 # Create a Galaxy work library/folder
76 # Combine the cycle, BTR and sample name as the base library name
77 lib_path = [p.strip() for p in f'{cycle}/{btr}/{sample}'.split('/')]
78 (library_id, folder_id, folder_names) = get_folder_id(gi, lib_path)
79 if not library_id:
80 library = gi.libraries.create_library(lib_path[0], description=None, synopsis=None)
81 library_id = library['id']
82 # if user:
83 # gi.libraries.set_library_permissions(library_id, access_ids=user,
84 # manage_ids=user, modify_ids=user)
85 logger.info(f'Created Library:\n{library}')
86 if len(folder_names):
87 folder = gi.libraries.create_folder(library_id, folder_names[0], description=None,
88 base_folder_id=folder_id)[0]
89 folder_id = folder['id']
90 logger.info(f'Created Folder:\n{folder}')
91 folder_names.pop(0)
92 while len(folder_names):
93 folder = gi.folders.create_folder(folder['id'], folder_names[0],
94 description=None)
95 folder_id = folder['id']
96 logger.info(f'Created Folder:\n{folder}')
97 folder_names.pop(0)
98
99 # Create a sym link for the Nexus file
100 dataset = gi.libraries.upload_from_galaxy_filesystem(library_id, path.abspath(filename),
101 folder_id=folder_id, file_type='auto', dbkey='?', link_data_only='link_to_files',
102 roles='', preserve_dirs=False, tag_using_filenames=False, tags=None)[0]
103
104 # Make a history for the data
105 history_name = f'tomo {btr} {sample}'
106 history = gi.histories.create_history(name=history_name)
107 logger.info(f'Created history:\n{history}')
108 history_id = history['id']
109 gi.histories.copy_dataset(history_id, dataset['id'], source='library')
110
111 # TODO add option to either
112 # get a URL to share the history
113 # or to share with specific users
114 # This might require using:
115 # https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/docs.html#using-bioblend-for-raw-api-calls
116