def iter_otus(nexson, nexson_version=None):
"""generator over all otus in all otus group elements.
yields a tuple of 3 items:
otus group ID,
otu ID,
the otu obj
"""
if nexson_version is None:
nexson_version = detect_nexson_version(nexson)
if not _is_by_id_hbf(nexson_version):
convert_nexson_format(
nexson, BY_ID_HONEY_BADGERFISH) # TODO shouldn't modify...
nex = get_nexml_el(nexson)
otus_group_by_id = nex['otusById']
group_order = nex.get('^ot:otusElementOrder', [])
if len(group_order) < len(otus_group_by_id):
group_order = list(otus_group_by_id.keys())
group_order.sort()
for otus_group_id in group_order:
otus_group = otus_group_by_id[otus_group_id]
otu_by_id = otus_group['otuById']
ti_order = list(otu_by_id.keys())
for otu_id in ti_order:
otu = otu_by_id[otu_id]
yield otus_group_id, otu_id, otu
def iter_trees(nexson, nexson_version=None):
'''generator over all trees in all trees elements.
yields a tuple of 3 items:
trees element ID,
tree ID,
the tree obj
'''
if nexson_version is None:
nexson_version = detect_nexson_version(nexson)
nex = get_nexml_el(nexson)
if _is_by_id_hbf(nexson_version):
trees_group_by_id = nex['treesById']
group_order = nex.get('^ot:treesElementOrder', [])
if len(group_order) < len(trees_group_by_id):
group_order = list(trees_group_by_id.keys())
group_order.sort()
for trees_group_id in group_order:
trees_group = trees_group_by_id[trees_group_id]
tree_by_id = trees_group['treeById']
ti_order = trees_group.get('^ot:treeElementOrder', [])
if len(ti_order) < len(tree_by_id):
ti_order = list(tree_by_id.keys())
ti_order.sort()
for tree_id in ti_order:
tree = tree_by_id[tree_id]
yield trees_group_id, tree_id, tree
else:
for trees_group in nex.get('trees', []):
trees_group_id = trees_group['@id']
for tree in trees_group.get('tree', []):
tree_id = tree['@id']
yield trees_group_id, tree_id, tree
def iter_trees(nexson, nexson_version=None):
'''generator over all trees in all trees elements.
yields a tuple of 3 items:
trees element ID,
tree ID,
the tree obj
'''
if nexson_version is None:
nexson_version = detect_nexson_version(nexson)
nex = get_nexml_el(nexson)
if _is_by_id_hbf(nexson_version):
trees_group_by_id = nex['treesById']
group_order = nex.get('^ot:treesElementOrder', [])
if len(group_order) < len(trees_group_by_id):
group_order = list(trees_group_by_id.keys())
group_order.sort()
for trees_group_id in group_order:
trees_group = trees_group_by_id[trees_group_id]
tree_by_id = trees_group['treeById']
ti_order = trees_group.get('^ot:treeElementOrder', [])
if len(ti_order) < len(tree_by_id):
ti_order = list(tree_by_id.keys())
ti_order.sort()
for tree_id in ti_order:
tree = tree_by_id[tree_id]
yield trees_group_id, tree_id, tree
else:
for trees_group in nex.get('trees', []):
trees_group_id = trees_group['@id']
for tree in trees_group.get('tree', []):
tree_id = tree['@id']
yield trees_group_id, tree_id, tree
def count_num_trees(nexson, nexson_version=None):
if nexson_version is None:
nexson_version = detect_nexson_version(nexson)
nex = get_nexml_el(nexson)
num_trees_by_group = []
if _is_by_id_hbf(nexson_version):
for tree_group in nex.get('treesById', {}).values():
nt = len(tree_group.get('treeById', {}))
num_trees_by_group.append(nt)
else:
trees_group = nex.get('trees', [])
if isinstance(trees_group, dict):
trees_group = [trees_group]
for tree_group in trees_group:
t = tree_group.get('tree')
if isinstance(t, list):
nt = len(t)
else:
nt = 1
num_trees_by_group.append(nt)
return sum(num_trees_by_group)
def gen_otu_dict(nex_obj, nexson_version=None):
"""Takes a NexSON object and returns a dict of
otu_id -> otu_obj
"""
if nexson_version is None:
nexson_version = detect_nexson_version(nex_obj)
if _is_by_id_hbf(nexson_version):
otus = nex_obj["nexml"]["otusById"]
if len(otus) > 1:
d = {}
for v in otus.values():
d.update(v["otuById"])
return d
else:
return otus.values()[0]["otuById"]
o_dict = {}
for ob in nex_obj.get("otus", []):
for o in ob.get("otu", []):
oid = o["@id"]
o_dict[oid] = o
return o_dict
def gen_otu_dict(nex_obj, nexson_version=None):
'''Takes a NexSON object and returns a dict of
otu_id -> otu_obj
'''
if nexson_version is None:
nexson_version = detect_nexson_version(nex_obj)
if _is_by_id_hbf(nexson_version):
otus = nex_obj['nexml']['otusById']
if len(otus) > 1:
d = {}
for v in otus.values():
d.update(v['otuById'])
return d
else:
return otus.value()[0]['otuById']
o_dict = {}
for ob in nex_obj.get('otus', []):
for o in ob.get('otu', []):
oid = o['@id']
o_dict[oid] = o
return o_dict
def gen_otu_dict(nex_obj, nexson_version=None):
'''Takes a NexSON object and returns a dict of
otu_id -> otu_obj
'''
if nexson_version is None:
nexson_version = detect_nexson_version(nex_obj)
if _is_by_id_hbf(nexson_version):
otus = nex_obj['nexml']['otusById']
if len(otus) > 1:
d = {}
for v in otus.values():
d.update(v['otuById'])
return d
else:
return otus.value()[0]['otuById']
o_dict = {}
for ob in nex_obj.get('otus', []):
for o in ob.get('otu', []):
oid = o['@id']
o_dict[oid] = o
return o_dict
def count_num_trees(nexson, nexson_version=None):
'''Returns the number of trees summed across all tree
groups.
'''
if nexson_version is None:
nexson_version = detect_nexson_version(nexson)
nex = get_nexml_el(nexson)
num_trees_by_group = []
if _is_by_id_hbf(nexson_version):
for tree_group in nex.get('treesById', {}).values():
nt = len(tree_group.get('treeById', {}))
num_trees_by_group.append(nt)
else:
trees_group = nex.get('trees', [])
if isinstance(trees_group, dict):
trees_group = [trees_group]
for tree_group in trees_group:
t = tree_group.get('tree')
if isinstance(t, list):
nt = len(t)
else:
nt = 1
num_trees_by_group.append(nt)
return sum(num_trees_by_group)
def iter_otus(nexson, nexson_version=None):
'''generator over all otus in all otus group elements.
yields a tuple of 3 items:
otus group ID,
otu ID,
the otu obj
'''
if nexson_version is None:
nexson_version = detect_nexson_version(nexson)
nex = get_nexml_el(nexson)
if not _is_by_id_hbf(nexson_version):
convert_nexson_format(nexson_blob, BY_ID_HONEY_BADGERFISH) #TODO shouldn't modify...
otus_group_by_id = nex['otusById']
group_order = nex.get('^ot:otusElementOrder', [])
if len(group_order) < len(otus_group_by_id):
group_order = list(otus_group_by_id.keys())
group_order.sort()
for otus_group_id in group_order:
otus_group = otus_group_by_id[otus_group_id]
otu_by_id = otus_group['otuById']
ti_order = list(otu_by_id.keys())
for otu_id in ti_order:
otu = otu_by_id[otu_id]
yield otus_group_id, otu_id, otu
