Mercurial > repos > rv43 > test_tomo_reconstruct

annotate workflow/link_to_galaxy.py @ 0:98e23dff1de2 draft default tip

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit f8c4bdb31c20c468045ad5e6eb255a293244bc6c-dirty
author rv43
date Tue, 21 Mar 2023 16:22:42 +0000
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1 #!/usr/bin/env python3
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2
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3 import logging
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4 logger = logging.getLogger(__name__)
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5
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6 from bioblend.galaxy import GalaxyInstance
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7 from nexusformat.nexus import *
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8 from os import path
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9 from yaml import safe_load
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10
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11 from .models import import_scanparser, TomoWorkflow
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12
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13 def get_folder_id(gi, path):
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14 library_id = None
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15 folder_id = None
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16 folder_names = path[1:] if len(path) > 1 else []
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17 new_folders = folder_names
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18 libs = gi.libraries.get_libraries(name=path[0])
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19 if libs:
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20 for lib in libs:
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21 library_id = lib['id']
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22 folders = gi.libraries.get_folders(library_id, folder_id=None, name=None)
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23 for i, folder in enumerate(folders):
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24 fid = folder['id']
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25 details = gi.libraries.show_folder(library_id, fid)
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26 library_path = details['library_path']
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27 if library_path == folder_names:
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28 return (library_id, fid, [])
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29 elif len(library_path) < len(folder_names):
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30 if library_path == folder_names[:len(library_path)]:
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31 nf = folder_names[len(library_path):]
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32 if len(nf) < len(new_folders):
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33 folder_id = fid
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34 new_folders = nf
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35 return (library_id, folder_id, new_folders)
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36
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37 def link_to_galaxy(filename:str, galaxy=None, user=None, password=None, api_key=None) -> None:
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38 # Read input file
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39 extension = path.splitext(filename)[1]
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40 # RV yaml input not incorporated yet, since Galaxy can't use pyspec right now
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41 # if extension == '.yml' or extension == '.yaml':
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42 # with open(filename, 'r') as f:
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43 # data = safe_load(f)
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44 # elif extension == '.nxs':
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45 if extension == '.nxs':
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46 with NXFile(filename, mode='r') as nxfile:
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47 data = nxfile.readfile()
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48 else:
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49 raise ValueError(f'Invalid filename extension ({extension})')
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50 if isinstance(data, dict):
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51 # Create Nexus format object from input dictionary
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52 wf = TomoWorkflow(**data)
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53 if len(wf.sample_maps) > 1:
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54 raise ValueError(f'Multiple sample maps not yet implemented')
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55 nxroot = NXroot()
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56 for sample_map in wf.sample_maps:
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57 import_scanparser(sample_map.station)
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58 # RV raw data must be included, since Galaxy can't use pyspec right now
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59 # sample_map.construct_nxentry(nxroot, include_raw_data=False)
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60 sample_map.construct_nxentry(nxroot, include_raw_data=True)
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61 nxentry = nxroot[nxroot.attrs['default']]
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62 elif isinstance(data, NXroot):
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63 nxentry = data[data.attrs['default']]
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64 else:
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65 raise ValueError(f'Invalid input file data ({data})')
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66
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67 # Get a Galaxy instance
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68 if user is not None and password is not None :
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69 gi = GalaxyInstance(url=galaxy, email=user, password=password)
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70 elif api_key is not None:
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71 gi = GalaxyInstance(url=galaxy, key=api_key)
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72 else:
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73 exit('Please specify either a valid Galaxy username/password or an API key.')
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74
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75 cycle = nxentry.instrument.source.attrs['cycle']
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76 btr = nxentry.instrument.source.attrs['btr']
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77 sample = nxentry.sample.name
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78
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79 # Create a Galaxy work library/folder
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80 # Combine the cycle, BTR and sample name as the base library name
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81 lib_path = [p.strip() for p in f'{cycle}/{btr}/{sample}'.split('/')]
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82 (library_id, folder_id, folder_names) = get_folder_id(gi, lib_path)
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83 if not library_id:
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84 library = gi.libraries.create_library(lib_path[0], description=None, synopsis=None)
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85 library_id = library['id']
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86 # if user:
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87 # gi.libraries.set_library_permissions(library_id, access_ids=user,
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88 # manage_ids=user, modify_ids=user)
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89 logger.info(f'Created Library:\n{library}')
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90 if len(folder_names):
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91 folder = gi.libraries.create_folder(library_id, folder_names[0], description=None,
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92 base_folder_id=folder_id)[0]
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93 folder_id = folder['id']
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94 logger.info(f'Created Folder:\n{folder}')
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95 folder_names.pop(0)
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96 while len(folder_names):
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97 folder = gi.folders.create_folder(folder['id'], folder_names[0],
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98 description=None)
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99 folder_id = folder['id']
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100 logger.info(f'Created Folder:\n{folder}')
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101 folder_names.pop(0)
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102
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103 # Create a sym link for the Nexus file
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104 dataset = gi.libraries.upload_from_galaxy_filesystem(library_id, path.abspath(filename),
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105 folder_id=folder_id, file_type='auto', dbkey='?', link_data_only='link_to_files',
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106 roles='', preserve_dirs=False, tag_using_filenames=False, tags=None)[0]
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107
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108 # Make a history for the data
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109 history_name = f'tomo {btr} {sample}'
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110 history = gi.histories.create_history(name=history_name)
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111 logger.info(f'Created history:\n{history}')
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112 history_id = history['id']
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113 gi.histories.copy_dataset(history_id, dataset['id'], source='library')
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114
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115 # TODO add option to either
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116 # get a URL to share the history
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117 # or to share with specific users
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118 # This might require using:
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119 # https://bioblend.readthedocs.io/en/latest/api_docs/galaxy/docs.html#using-bioblend-for-raw-api-calls
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120