Unverified Commit 8a7ca520 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Fix setting metadata for some Loom files 

Loom files created by recent versions of LoomExperiment Bioconductor
package encode the Loom version in an binary array, which breaks
metadata setting in Galaxy.
parent 5cc70512

lib/galaxy/datatypes/binary.py

+7 −1
Original line number Diff line number Diff line
@@ -16,6 +16,7 @@ from json import dumps 
from typing import Optional



import h5py

import numpy as np

import pysam

import pysam.bcftools

from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP
@@ -928,7 +929,12 @@ class Loom(H5): 
                dataset.metadata.description = loom_file.attrs.get('description')

                dataset.metadata.url = loom_file.attrs.get('url')

                dataset.metadata.doi = loom_file.attrs.get('doi')

                dataset.metadata.loom_spec_version = loom_file.attrs.get('LOOM_SPEC_VERSION')

                loom_spec_version = loom_file.attrs.get('LOOM_SPEC_VERSION')

                if isinstance(loom_spec_version, np.ndarray):

                    loom_spec_version = loom_spec_version[0]

                    if isinstance(loom_spec_version, bytes):

                        loom_spec_version = loom_spec_version.decode()

                dataset.metadata.loom_spec_version = loom_spec_version

                dataset.creation_date = loom_file.attrs.get('creation_date')

                dataset.metadata.shape = tuple(loom_file['matrix'].shape)