Merge pull request #17582 from muon-spectroscopy-computational-projec…

…t/33_fix_cif_sniff_23.2

[23.2] Account for newlines in CIF Datatype sniffer

lib/galaxy/datatypes/molecules.py

@@ -1009,6 +1009,9 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         >>> fname = get_test_fname('1.star')
         >>> CIF().sniff(fname)
         False
+        >>> fname = get_test_fname('LaMnO3.cif')
+        >>> CIF().sniff(fname)
+        True
         """
 
         # check for optional CIF version marker '#\#CIF_<version>' at start of file
@@ -1019,7 +1022,7 @@ def sniff_prefix(self, file_prefix: FilePrefix) -> bool:
         # first non-comment line must begin with 'data_'
         # and '_atom_site_fract_(x|y|z)' must be specified somewhere in the file
         for line in file_prefix.line_iterator():
-            if not line:
+            if not line.rstrip():
                 continue
             elif line[0] == "#":  # comment so skip
                 continue

lib/galaxy/datatypes/sniff.py

@@ -399,6 +399,9 @@ def guess_ext(fname_or_file_prefix: Union[str, "FilePrefix"], sniff_order, is_bi
     >>> fname = get_test_fname('Si.cif')
     >>> guess_ext(fname, sniff_order)
     'cif'
+    >>> fname = get_test_fname('LaMnO3.cif')
+    >>> guess_ext(fname, sniff_order)
+    'cif'
     >>> fname = get_test_fname('Si.xyz')
     >>> guess_ext(fname, sniff_order)
     'xyz'

lib/galaxy/datatypes/test/LaMnO3.cif

@@ -0,0 +1,66 @@
+####################################################################### 
+# 
+# This file contains crystal structure data downloaded from the 
+# Cambridge Structural Database (CSD) hosted by the Cambridge 
+# Crystallographic Data Centre (CCDC) in cooperation with FIZ Karlsruhe.
+# 
+# Please note that these data are only for research purposes or private use.
+# For detailed information please see under Terms & Conditions.
+# Full information about CCDC and FIZ Karlsruhe data access policies and 
+# citation guidelines are available at http://www.ccdc.cam.ac.uk/access/V1
+# 
+# Audit and citation data items may have been added by FIZ Karlsruhe. 
+# Please retain this information to preserve the provenance of 
+# this file and to allow appropriate attribution of the data. 
+# 
+#######################################################################
+
+data_150259-ICSD
+_database_code_depnum_ccdc_archive 'CCDC 1667441'
+loop_
+_citation_id
+_citation_doi
+_citation_year
+1 10.1006/jssc.2001.9440 2002
+_audit_update_record             
+;
+2018-02-27 deposited with the CCDC.	2024-01-08 downloaded from the CCDC.
+;
+_database_code_ICSD              150259
+_chemical_name_systematic        'Lanthanum Manganate'
+_chemical_formula_sum            'La1 Mn1 O3'
+_cell_length_a                   5.486
+_cell_length_b                   7.761
+_cell_length_c                   5.487
+_cell_angle_alpha                90
+_cell_angle_beta                 90
+_cell_angle_gamma                90.01
+_cell_volume                     233.62
+_cell_formula_units_Z            4
+_symmetry_space_group_name_H-M   'I 1 1 2/b'
+_symmetry_Int_Tables_number      15
+_symmetry_cell_setting           monoclinic
+_refine_ls_R_factor_all          0.03
+loop_
+_symmetry_equiv_pos_site_id
+_symmetry_equiv_pos_as_xyz
+1 '-x, -y+1/2, z'
+2 'x, y+1/2, -z'
+3 '-x, -y, -z'
+4 'x, y, z'
+5 '-x+1/2, -y, z+1/2'
+6 'x+1/2, y, -z+1/2'
+7 '-x+1/2, -y+1/2, -z+1/2'
+8 'x+1/2, y+1/2, z+1/2'
+loop_
+_atom_site_label
+_atom_site_type_symbol
+_atom_site_fract_x
+_atom_site_fract_y
+_atom_site_fract_z
+La1 La3+ 0 0.25 0.5052
+Mn1 Mn3+ 0 0 0
+O1 O2- 0 0.25 0.0015
+O2 O2- 0.2682 0.0015 0.2427
+
+#End of data_150259-ICSD