def _post_key_check_validate_otus_obj(self, og_nex_id, otus_group, vc):
otu_obj = otus_group.get('otuById', {})
if not isinstance(otu_obj, dict):
self._error_event(_NEXEL.OTUS,
obj=otus_group,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=og_nex_id,
key_list=['otuById'])
return errorReturn('no "otuById" in otus group')
self._otu_group_by_id[og_nex_id] = otus_group
vc.push_context(_NEXEL.OTU, (otus_group, og_nex_id))
try:
not_dict_otu = []
ndo_id_list = []
otu_id_obj_list = []
for id_obj_pair in otu_obj.items():
if not isinstance(id_obj_pair[1], dict):
r = check_raw_dict(id_obj_pair[1], otus_group, None, vc)
assert r[0] is False
t = r[1]
not_dict_otu.append(t)
ndo_id_list.append(id_obj_pair[0])
else:
otu_id_obj_list.append(id_obj_pair)
if not_dict_otu:
self._error_event(_NEXEL.OTU,
obj=otu_obj,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=ndo_id_list,
key_val_type_list=[not_dict_otu])
return errorReturn('otu is wrong type')
r = self._validate_otu_list(otu_id_obj_list, vc)
if r:
self._otu_by_otug[og_nex_id] = otu_obj
return r
finally:
vc.pop_context()
def _post_key_check_validate_otus_obj(self, og_nex_id, otus_group, vc):
otu_obj = otus_group.get('otuById', {})
if not isinstance(otu_obj, dict):
self._error_event(_NEXEL.OTUS,
obj=otus_group,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=og_nex_id,
key_list=['otuById'])
return errorReturn('no "otuById" in otus group')
self._otu_group_by_id[og_nex_id] = otus_group
vc.push_context(_NEXEL.OTU, (otus_group, og_nex_id))
try:
not_dict_otu = []
ndo_id_list = []
otu_id_obj_list = []
for id_obj_pair in otu_obj.items():
if not isinstance(id_obj_pair[1], dict):
r = check_raw_dict(id_obj_pair[1], otus_group, None, vc)
assert r[0] is False
t = r[1]
not_dict_otu.append(t)
ndo_id_list.append(id_obj_pair[0])
else:
otu_id_obj_list.append(id_obj_pair)
if not_dict_otu:
self._error_event(_NEXEL.OTU,
obj=otu_obj,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=ndo_id_list,
key_val_type_list=[not_dict_otu])
return errorReturn('otu is wrong type')
r = self._validate_otu_list(otu_id_obj_list, vc)
if r:
self._otu_by_otug[og_nex_id] = otu_obj
return r
finally:
vc.pop_context()
def _post_key_check_validate_nexml_obj(self, nex_obj, obj_nex_id, vc):
otus = nex_obj.get('otusById', {})
otus_order_list = nex_obj.get('^ot:otusElementOrder', [])
if not isinstance(otus, dict) or (otus_order_list and (not otus)):
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=['otusById'])
return errorReturn('Missing "otusById"')
if (not isinstance(otus_order_list, list)) or ((not otus_order_list) and otus):
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=['^ot:otusElementOrder'])
return errorReturn('Missing "^ot:otusElementOrder"')
otus_group_list = []
missing_ogid = []
not_dict_og = []
for ogid in otus_order_list:
og = otus.get(ogid)
if og is None:
missing_ogid.append(ogid)
elif not isinstance(og, dict):
r = check_raw_dict(og, otus, ogid, vc)
assert r[0] is False
t = r[1]
not_dict_og.append(t)
else:
otus_group_list.append((ogid, og))
if missing_ogid:
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_ReferencedIDNotFoundWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=missing_ogid)
return errorReturn('Missing "@id" for otus group')
vc.push_context(_NEXEL.OTUS, (nex_obj, obj_nex_id))
try:
if not_dict_og:
self._error_event(_NEXEL.OTUS,
obj=otus,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=None,
key_val_type_list=[not_dict_og])
return errorReturn('Otus objects of the wrong type of object')
if not self._validate_otus_group_list(otus_group_list, vc):
return False
finally:
vc.pop_context()
# and now the trees...
trees = nex_obj.get('treesById')
trees_order_list = nex_obj.get('^ot:treesElementOrder')
if (not isinstance(trees, dict)) or ((not trees) and trees_order_list):
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_MissingCrucialContentWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=['treesById'])
return errorReturn('Missing "treesById"')
if (not isinstance(trees_order_list, list)) or ((not trees_order_list) and trees):
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_MissingCrucialContentWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=['^ot:treesElementOrder'])
return errorReturn('Missing "^ot:treesElementOrder"')
trees_group_list = []
missing_tgid = []
not_dict_tg = []
for tgid in trees_order_list:
tg = trees.get(tgid)
if tg is None:
missing_tgid.append(tgid)
elif not isinstance(tg, dict):
r = check_raw_dict(tg, trees, tgid, vc)
assert r[0] is False
t = r[1]
not_dict_tg.append(t)
else:
trees_group_list.append((tgid, tg))
if missing_tgid:
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_ReferencedIDNotFoundWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=missing_tgid)
return errorReturn('Missing trees group id')
vc.push_context(_NEXEL.TREES, (nex_obj, obj_nex_id))
try:
if not_dict_tg:
self._error_event(_NEXEL.TREES,
obj=trees,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=None,
key_val_type_list=[not_dict_tg])
return errorReturn('Trees element of the wrong type')
if not self._validate_trees_group_list(trees_group_list, vc):
return False
finally:
vc.pop_context()
if not nex_obj.get('ot:notIntendedForSynthesis'):
cs = nex_obj.get('ot:candidateTreeForSynthesis')
if cs:
if not isinstance(cs, list):
tree_list = [cs]
else:
tree_list = cs
else:
tree_list = []
for tg in trees.values():
tbi = tg.get('treeById', {})
tree_list.extend(tbi.keys())
self._generate_ott_warnings(otus, tree_list, (nex_obj, obj_nex_id), vc)
return True
def _post_key_check_validate_nexml_obj(self, nex_obj, obj_nex_id, vc):
otus = nex_obj.get('otusById', {})
otus_order_list = nex_obj.get('^ot:otusElementOrder', [])
if not isinstance(otus, dict) or (otus_order_list and (not otus)):
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=['otusById'])
return errorReturn('Missing "otusById"')
if (not isinstance(otus_order_list, list)) or ((not otus_order_list)
and otus):
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=['^ot:otusElementOrder'])
return errorReturn('Missing "^ot:otusElementOrder"')
otus_group_list = []
missing_ogid = []
not_dict_og = []
for ogid in otus_order_list:
og = otus.get(ogid)
if og is None:
missing_ogid.append(ogid)
elif not isinstance(og, dict):
r = check_raw_dict(og, otus, ogid, vc)
assert r[0] is False
t = r[1]
not_dict_og.append(t)
else:
otus_group_list.append((ogid, og))
if missing_ogid:
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_ReferencedIDNotFoundWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=missing_ogid)
return errorReturn('Missing "@id" for otus group')
vc.push_context(_NEXEL.OTUS, (nex_obj, obj_nex_id))
try:
if not_dict_og:
self._error_event(_NEXEL.OTUS,
obj=otus,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=None,
key_val_type_list=[not_dict_og])
return errorReturn('Otus objects of the wrong type of object')
if not self._validate_otus_group_list(otus_group_list, vc):
return False
finally:
vc.pop_context()
# and now the trees...
trees = nex_obj.get('treesById')
trees_order_list = nex_obj.get('^ot:treesElementOrder')
if (not isinstance(trees, dict)) or ((not trees) and trees_order_list):
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_MissingCrucialContentWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=['treesById'])
return errorReturn('Missing "treesById"')
if (not isinstance(trees_order_list, list)) or ((not trees_order_list)
and trees):
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_MissingCrucialContentWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=['^ot:treesElementOrder'])
return errorReturn('Missing "^ot:treesElementOrder"')
trees_group_list = []
missing_tgid = []
not_dict_tg = []
for tgid in trees_order_list:
tg = trees.get(tgid)
if tg is None:
missing_tgid.append(tgid)
elif not isinstance(tg, dict):
r = check_raw_dict(tg, trees, tgid, vc)
assert r[0] is False
t = r[1]
not_dict_tg.append(t)
else:
trees_group_list.append((tgid, tg))
if missing_tgid:
self._error_event(_NEXEL.NEXML,
obj=nex_obj,
err_type=gen_ReferencedIDNotFoundWarning,
anc=vc.anc_list,
obj_nex_id=obj_nex_id,
key_list=missing_tgid)
return errorReturn('Missing trees group id')
vc.push_context(_NEXEL.TREES, (nex_obj, obj_nex_id))
try:
if not_dict_tg:
self._error_event(_NEXEL.TREES,
obj=trees,
err_type=gen_WrongValueTypeWarning,
anc=vc.anc_list,
obj_nex_id=None,
key_val_type_list=[not_dict_tg])
return errorReturn('Trees element of the wrong type')
if not self._validate_trees_group_list(trees_group_list, vc):
return False
finally:
vc.pop_context()
if not nex_obj.get('ot:notIntendedForSynthesis'):
cs = nex_obj.get('ot:candidateTreeForSynthesis')
if cs:
if not isinstance(cs, list):
tree_list = [cs]
else:
tree_list = cs
else:
tree_list = []
for tg in trees.values():
tbi = tg.get('treeById', {})
tree_list.extend(tbi.keys())
self._generate_ott_warnings(otus, tree_list, (nex_obj, obj_nex_id),
vc)
return True