@@ -476,6 +476,8 @@ def graph_elems(self):
476476
477477 if hasattr (self , 'bald__array' ):
478478 for aref in self .bald__array :
479+ if isinstance (aref , str ):
480+ raise TypeError ('unexpected string: {}' .format (aref ))
479481 alink = "link({var}, {target}, 'bald__array', 'bottom');"
480482 alink = alink .format (var = self .identity , target = aref .identity )
481483 links .append (alink )
@@ -511,19 +513,6 @@ def graph_elems(self):
511513 return instances , links
512514
513515
514- @contextlib .contextmanager
515- def load (afilepath ):
516- if afilepath .endswith ('.hdf' ):
517- loader = h5py .File
518- else :
519- raise ValueError ('filepath suffix not supported' )
520- try :
521- f = loader (afilepath , "r" )
522- yield f
523- finally :
524- f .close ()
525-
526-
527516@contextlib .contextmanager
528517def load (afilepath ):
529518 if afilepath .endswith ('.hdf' ):
@@ -540,11 +529,13 @@ def load(afilepath):
540529
541530def load_netcdf (afilepath , baseuri = None ):
542531 """
543- Validate a file with respect to binary-array-linked-data.
544- Returns a :class:`bald.validation.Validation `
532+ Load a file with respect to binary-array-linked-data.
533+ Returns a :class:`bald.Collection `
545534 """
546535
547536 with load (afilepath ) as fhandle :
537+ if baseuri is None :
538+ baseuri = 'file://{}' .format (afilepath )
548539 prefix_var_name = None
549540 if hasattr (fhandle , 'bald__isPrefixedBy' ):
550541 prefix_var_name = fhandle .bald__isPrefixedBy
@@ -609,8 +600,7 @@ def load_netcdf(afilepath, baseuri=None):
609600 # netCDF coordinate variable special case
610601 if (len (fhandle .variables [name ].dimensions ) == 1 and
611602 fhandle .variables [name ].dimensions [0 ] == name ):
612- #sattrs['bald__array'] = name
613- sattrs ['bald__array' ] = identity
603+ sattrs ['bald__array' ] = name
614604 sattrs ['rdf__type' ] = 'bald__Reference'
615605
616606 if fhandle .variables [name ].shape :
@@ -629,18 +619,42 @@ def load_netcdf(afilepath, baseuri=None):
629619 continue
630620
631621 var = file_variables [name ]
632- # reverse lookup based on type to be added
633- lookups = ['bald__references' , 'bald__array' ]
634- for lookup in lookups :
635- if lookup in var .attrs :
636- child_dset_set = var .attrs [lookup ].split (' ' )
637- var .attrs [lookup ] = set ()
638- for child_dset_name in child_dset_set :
639- carray = file_variables .get (child_dset_name )
640- var .attrs [lookup ].add (carray )
622+ sattrs = fhandle .variables [name ].__dict__ .copy ()
623+ # netCDF coordinate variable special case
624+ if (len (fhandle .variables [name ].dimensions ) == 1 and
625+ fhandle .variables [name ].dimensions [0 ] == name ):
626+ sattrs ['bald__array' ] = name
627+
628+ for sattr in sattrs :
629+ if (isinstance (sattrs [sattr ], str ) and
630+ file_variables .get (sattrs [sattr ])):
631+ # next: remove all use of set, everything is dict or orderedDict
632+ var .attrs [sattr ] = set ((file_variables .get (sattrs [sattr ]),))
633+ elif isinstance (sattrs [sattr ], str ):
634+ potrefs_list = sattrs [sattr ].split (',' )
635+ potrefs_set = sattrs [sattr ].split (' ' )
636+ if len (potrefs_list ) > 1 :
637+ refs = np .array ([file_variables .get (pref ) is not None
638+ for pref in potrefs_list ])
639+ if np .all (refs ):
640+ var .attrs [sattr ] = [file_variables .get (pref )
641+ for pref in potrefs_list ]
642+
643+ elif len (potrefs_set ) > 1 :
644+ refs = np .array ([file_variables .get (pref ) is not None
645+ for pref in potrefs_set ])
646+ if np .all (refs ):
647+ var .attrs [sattr ] = set ([file_variables .get (pref )
648+ for pref in potrefs_set ])
649+
650+ # if name == 'pdim0':
651+ # import pdb; pdb.set_trace()
652+
641653 # coordinate variables are bald__references except for
642654 # variables that already declare themselves as bald__Reference
643655 if 'bald__Reference' not in var .rdf__type :
656+ # if name == 'pdim0':
657+ # import pdb; pdb.set_trace()
644658 for dim in fhandle .variables [name ].dimensions :
645659 if file_variables .get (dim ):
646660 cv_shape = fhandle .variables [dim ].shape
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