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sniff tests and 'no ase' message

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elichad
2022-04-01 09:35:04 +00:00
parent 4fa9ee2d02
commit b46072ee1d
2 changed files with 30 additions and 7 deletions
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lib/galaxy/datatypes/molecules.py
+17 -6
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@@ -957,7 +957,11 @@ class Cell(GenericMolFile):
info_list.append(f"Atoms in file:\n{metadata.number_of_atoms}")
info += "\n--\n".join(info_list)
else:
info += f"Atoms in file:\n{metadata.number_of_atoms}"
info = """
Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
You can still use this dataset in tools and workflows.
For full metadata, ask your admin to install the 'ase' Python package.
"""
return info
@@ -1156,8 +1160,12 @@ class CIF(GenericMolFile):
formulae = "\n".join(metadata.chemical_formula)
info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
info = "\n--\n".join(info_list)
# else:
# info = f"Atoms in file:\n{metadata.number_of_atoms}"
else:
info = """
Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
You can still use this dataset in tools and workflows.
For full metadata, ask your admin to install the 'ase' Python package.
"""
return info
@@ -1365,9 +1373,12 @@ class XYZ(GenericMolFile):
formulae = "\n".join(metadata.chemical_formula)
info_list.append(f"Chemical formula for each structure in this file:\n{formulae}")
info = "\n--\n".join(info_list)
# else:
# TODO: message along the lines of "ask your admin to install ase"?
# info = f"Atoms in file:\n{metadata.number_of_atoms}"
else:
info = """
Metadata is limited as the Atomic Simulation Environment (ASE) is not installed.
You can still use this dataset in tools and workflows.
For full metadata, ask your admin to install the 'ase' Python package.
"""
return info
lib/galaxy/datatypes/sniff.py
+13 -1
View File
@@ -372,7 +372,10 @@ def guess_ext(fname, sniff_order, is_binary=False):
>>> fname = get_test_fname('5e5z.pdb')
>>> guess_ext(fname, sniff_order)
'pdb'
>>> fname = get_test_fname('Si.cell')
>>> fname = get_test_fname('Si_uppercase.cell')
>>> guess_ext(fname, sniff_order)
'cell'
>>> fname = get_test_fname('Si_lowercase.cell')
>>> guess_ext(fname, sniff_order)
'cell'
>>> fname = get_test_fname('Si.cif')
@@ -381,6 +384,15 @@ def guess_ext(fname, sniff_order, is_binary=False):
>>> fname = get_test_fname('Si.xyz')
>>> guess_ext(fname, sniff_order)
'xyz'
>>> fname = get_test_fname('Si_multi.xyz')
>>> guess_ext(fname, sniff_order)
'xyz'
>>> fname = get_test_fname('Si.extxyz')
>>> guess_ext(fname, sniff_order)
'extxyz'
>>> fname = get_test_fname('Si_multi.extxyz')
>>> guess_ext(fname, sniff_order)
'extxyz'
>>> fname = get_test_fname('mothur_datatypetest_true.mothur.otu')
>>> guess_ext(fname, sniff_order)
'mothur.otu'