qry = (
"match (t:term {nanoid:$nanoid}) "
"where not exists(t._to) "
- "with t "
- "optional match (t)-[:has_origin]->(o:origin) "
+ "with t, t.origin_name as origin_name "
+ "optional match (o:origin {name: origin_name}) "
"where not exists(o._to) "
"return t as term, o as origin "
)
diff --git a/docs/_modules/bento_meta/object_map.html b/docs/_modules/bento_meta/object_map.html
index 78c70ad..a375f93 100644
--- a/docs/_modules/bento_meta/object_map.html
+++ b/docs/_modules/bento_meta/object_map.html
@@ -104,7 +104,7 @@ Source code for bento_meta.object_map
# from pdb import set_trace
-[docs]class ObjectMap(object):
+[docs]class ObjectMap(object):
"""This module contains :class:`ObjectMap`, a class which provides the
machinery for mapping bento_meta objects to a Bento Metamodel Database
in Neo4j. Mostly not for human consumption."""
@@ -123,11 +123,11 @@ Source code for bento_meta.object_map
)
self.maps = {}
-[docs] @classmethod
+
-[docs] @classmethod
+[docs] @classmethod
def cls_by_label(cls, lbl):
if not hasattr(cls, "_clsxlbl"):
cls._clsxlbl = {}
@@ -135,7 +135,7 @@ Source code for bento_meta.object_map
cls._clsxlbl[o.mapspec()["label"]] = o
return cls._clsxlbl.get(lbl)
-[docs] @classmethod
+[docs] @classmethod
def keys_by_cls_and_reln(cls, qcls, reln):
if not hasattr(cls, "_keysxcls"):
cls._keysxcls = {}
@@ -150,7 +150,7 @@ Source code for bento_meta.object_map
cls._keysxcls[(o.__name__, r)] = (catt, o.mapspec()["key"])
return cls._keysxcls.get((qcls.__name__, reln))
-[docs] @classmethod
+[docs] @classmethod
def _quote_val(cls, value, single=None): # double quote unless single is set
if value is None:
return
@@ -162,7 +162,7 @@ Source code for bento_meta.object_map
else:
return '"{val}"'.format(val=value) # quote
-[docs] def get_by_id(self, obj, id, refresh=False):
+[docs] def get_by_id(self, obj, id, refresh=False):
"""Get an entity given an id attribute value (not the Neo4j id)"""
neoid = None
@@ -184,7 +184,7 @@ Source code for bento_meta.object_map
else:
return
-[docs] def get_by_node_nanoid(self, obj, nanoid, refresh=False):
+[docs] def get_by_node_nanoid(self, obj, nanoid, refresh=False):
"""PROTOTYPE
Get an entity given an id attribute value (not the Neo4j id)
"""
@@ -208,7 +208,7 @@ Source code for bento_meta.object_map
else:
return
-[docs] def get(self, obj, refresh=False):
+[docs] def get(self, obj, refresh=False):
"""Get the data for an object instance from the db and load the instance with it"""
if not self.drv:
raise ArgError("get() requires Neo4j driver instance")
@@ -279,7 +279,7 @@ Source code for bento_meta.object_map
obj.dirty = 0
return obj
-[docs] def put(self, obj):
+[docs] def put(self, obj):
"""Put the object instance's attributes to the mapped data node in the database"""
if not self.drv:
raise ArgError("put() requires Neo4j driver instance")
@@ -329,7 +329,7 @@ Source code for bento_meta.object_map
obj.dirty = 0
return obj
-[docs] def rm(self, obj, force=False):
+[docs] def rm(self, obj, force=False):
"""'Delete' the object's mapped node from the database"""
if not self.drv:
raise ArgError("rm() requires Neo4j driver instance")
@@ -343,7 +343,7 @@ Source code for bento_meta.object_map
else:
return s.value()
-[docs] def add(self, obj, att, tgt):
+[docs] def add(self, obj, att, tgt):
"""Create a link between an object instance and a target object in the database.
This represents adding an object-valued attribute to the object.
"""
@@ -357,7 +357,7 @@ Source code for bento_meta.object_map
warn("add() - corresponding db node not found")
return tgt_id
-[docs] def drop(self, obj, att, tgt, tx=None):
+[docs] def drop(self, obj, att, tgt, tx=None):
"""Remove an existing link between an object instance and a target object in the database.
This represents dropping an object-valued attribute from the object.
"""
@@ -387,7 +387,7 @@ Source code for bento_meta.object_map
else:
return s.value()
-[docs] def get_owners(self, obj):
+[docs] def get_owners(self, obj):
"""Get the nodes which are linked to the object instance (the owners of the object)"""
if not self.drv:
raise ArgError("get_owners() requires Neo4j driver instance")
@@ -411,7 +411,7 @@ Source code for bento_meta.object_map
ret.append((o, keys))
return ret
-[docs] def get_q(self, obj):
+[docs] def get_q(self, obj):
if not isinstance(obj, self.cls):
raise ArgError(
"arg1 must be object of class {cls}".format(cls=self.cls.__name__)
@@ -422,16 +422,16 @@ Source code for bento_meta.object_map
lbl=self.cls.mapspec()["label"], neoid=obj.neoid
)
-[docs] def get_by_id_q(self):
+[docs] def get_by_id_q(self):
return "MATCH (n:{lbl}) WHERE id(n)=$id and n._to IS NULL RETURN id(n)".format(
lbl=self.cls.mapspec()["label"]
)
-[docs] def get_by_node_nanoid_q(self):
+[docs] def get_by_node_nanoid_q(self):
"""PROTOTYPE"""
return "MATCH (n:node) WHERE n.nanoid=$nanoid and n._to is NULL RETURN id(n)"
-[docs] def get_attr_q(self, obj, att):
+[docs] def get_attr_q(self, obj, att):
if not isinstance(obj, self.cls):
raise ArgError(
"arg1 must be object of class {cls}".format(cls=self.cls.__name__)
@@ -473,7 +473,7 @@ Source code for bento_meta.object_map
)
)
-[docs] def get_owners_q(self, obj):
+[docs] def get_owners_q(self, obj):
if not isinstance(obj, self.cls):
raise ArgError(
"arg1 must be object of class {cls}".format(cls=self.cls.__name__)
@@ -485,7 +485,7 @@ Source code for bento_meta.object_map
neoid=obj.neoid, lbl=label
)
-[docs] def put_q(self, obj):
+[docs] def put_q(self, obj):
if not isinstance(obj, self.cls):
raise ArgError(
"arg1 must be object of class {cls}".format(cls=self.cls.__name__)
@@ -531,7 +531,7 @@ Source code for bento_meta.object_map
% (self.cls.mapspec()["label"], spec)
]
-[docs] def put_attr_q(self, obj, att, values):
+[docs] def put_attr_q(self, obj, att, values):
if not isinstance(obj, self.cls):
raise ArgError(
"arg1 must be object of class {cls}".format(cls=self.cls.__name__)
@@ -604,7 +604,7 @@ Source code for bento_meta.object_map
)
)
-[docs] def rm_q(self, obj, detach=False):
+[docs] def rm_q(self, obj, detach=False):
if not isinstance(obj, self.cls):
raise ArgError(
"arg1 must be object of class {cls}".format(cls=self.cls.__name__)
@@ -618,7 +618,7 @@ Source code for bento_meta.object_map
return qry + dlt
pass
-[docs] def rm_attr_q(self, obj, att, values=None):
+[docs] def rm_attr_q(self, obj, att, values=None):
if not isinstance(obj, self.cls):
raise ArgError(
"arg1 must be object of class {cls}".format(cls=self.cls.__name__)
@@ -693,7 +693,7 @@ Source code for bento_meta.object_map
)
)
-[docs] def _check_values_list(self, att, values):
+[docs] def _check_values_list(self, att, values):
v = values
if isinstance(values, CollValue):
v = values.values()
diff --git a/docs/_sources/mdb-conventions.rst.txt b/docs/_sources/mdb-conventions.rst.txt
index d35a258..f07e7e3 100644
--- a/docs/_sources/mdb-conventions.rst.txt
+++ b/docs/_sources/mdb-conventions.rst.txt
@@ -81,7 +81,7 @@ _______________________________________________
For integration with the STS, and for performance, the Neo4j instance
of an MDB requires certain indexes to be established. These are
-specified in `these Cypher statements `_. The primary
+specified in `these Cypher statements `_. The primary
requirement is that fulltext, Lucene-based indexes should be created
on entity ``description`` and Term ``origin_definition`` properties to
enable "search box" like queries over the the entire graph. Regular
@@ -120,7 +120,7 @@ on `Cypher MDB entity properties required for consistency
For integration with the STS, and for performance, the Neo4j instance
of an MDB requires certain indexes to be established. These are
-specified in these Cypher statements. The primary
+specified in these Cypher statements. The primary
requirement is that fulltext, Lucene-based indexes should be created
on entity description and Term origin_definition properties to
enable “search box” like queries over the the entire graph. Regular
@@ -200,7 +200,7 @@
Uniqueness and Existence of Entitiesbento_meta.entity", "bento_meta", "bento_meta.mdb", "bento_meta.mdb.loaders", "bento_meta.mdb.mdb", "bento_meta.mdb.mdb_tools", "bento_meta.mdb.mdb_tools.mdb_tools", "bento_meta.mdb.searchable", "bento_meta.mdb.writeable", "bento_meta.model", "bento_meta.object_map", "bento_meta.objects", "bento_meta.util._engine", "bento_meta.util.cypher.clauses", "bento_meta.util.cypher.entities", "bento_meta.util.cypher.functions", "bento_meta.util.cypher", "bento_meta.util", "bento_meta.util.makeq", "API Reference", "Loading an MDB instance", "bento_meta and Metamodel Database (MDB)", "MDB Conventions and Patterns", "Metamodel Database (MDB) Principles", "bento_meta and MDF", "Model Versioning", "Object Map Specifications", "The Object Model"], "terms": {"provid": [0, 10, 21, 22, 23, 24, 26, 27], "an": [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 14, 18, 21, 22, 23, 26], "represent": [13, 14, 15, 21, 23, 27], "graph": [0, 9, 14, 21, 23, 24, 26, 27], "base": [0, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 21, 22, 23, 26, 27], "data": [2, 4, 9, 10, 11, 21, 22, 23, 24, 26, 27], "model": [0, 1, 2, 3, 4, 10, 11, 19, 21, 26], "embodi": 21, "structur": [21, 22, 24, 27], "bento": [1, 2, 5, 6, 8, 9, 10, 21, 22, 24], "The": [0, 2, 4, 8, 9, 10, 21, 22, 23, 24, 25, 26], "can": [9, 21, 22, 23, 24, 25, 26, 27], "store": [0, 21, 22, 23, 25, 27], "multipl": [21, 23, 24, 27], "term": [2, 4, 5, 6, 7, 8, 9, 11, 21, 23, 24], "relationship": [2, 4, 5, 6, 7, 11, 14, 21, 22, 23, 24, 26, 27], "link": [5, 6, 9, 10, 11, 21, 22, 23, 26, 27], "entiti": [1, 2, 3, 4, 5, 6, 7, 9, 10, 11, 16, 17, 19, 21, 24, 27], "accord": [21, 22, 24, 27], "individu": [21, 23, 27], "For": [21, 22, 23, 27], "exampl": [21, 22, 23, 24, 26, 27], "ar": [0, 2, 4, 9, 10, 11, 21, 22, 23, 24, 27], "repres": [2, 4, 5, 6, 8, 10, 11, 13, 17, 21, 22, 23, 26, 27], "type": [0, 5, 6, 9, 11, 14, 21, 23, 24, 26, 27], "appropri": [10, 21, 22, 23, 26], "sourc": [0, 2, 3, 4, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 21, 22, 23, 24, 26, 27], "destin": [21, 24, 26, 27], "class": [21, 23, 26, 27], "creat": [0, 2, 3, 4, 5, 6, 8, 9, 10, 13, 17, 19, 21, 22, 23, 24, 25, 26, 27], "read": [2, 4, 21, 23], "updat": [0, 21, 23], "togeth": 21, "push": [9, 21, 24, 26, 27], "pull": [9, 21, 22, 24, 26, 27], "them": [5, 6, 10, 21, 27], "from": [0, 2, 3, 4, 5, 6, 9, 10, 11, 17, 18, 21, 22, 23, 24, 25, 27], "back": [21, 22, 23, 27], "neo4j": [0, 2, 4, 7, 9, 10, 13, 18, 21, 22, 24, 26, 27], "also": [0, 2, 4, 21, 22, 23, 24, 26, 27], "defin": [0, 14, 21, 22, 23, 24], "maintain": [21, 22], "terminologi": [11, 21, 22, 23, 27], "associ": [2, 4, 8, 9, 10, 21, 22, 23, 24, 26], "These": [21, 22, 23, 26, 27], "includ": [21, 22, 23, 24, 26], "themselv": [10, 21, 22, 23, 27], "origin": [2, 4, 8, 11, 21, 22, 23, 27], "concept": [5, 6, 9, 11, 21, 22, 23, 26, 27], "predic": [5, 6, 11, 21, 23, 27], "each": [2, 4, 5, 6, 10, 21, 22, 23, 24, 26, 27], "us": [0, 2, 4, 5, 6, 9, 11, 21, 22, 23, 24, 26, 27], "run": [2, 4, 8, 21], "pip": [21, 24], "http": [2, 4, 24], "github": [2, 8, 22, 24], "com": [2, 4, 24], "cbiit": 24, "meta": [1, 2, 5, 6, 8, 21], "raw": [], "master": [], "python": [2, 4, 21, 22, 24], "dist": [], "0": [5, 6], "2": [25, 27], "tar": [], "gz": [], "principl": [21, 22], "motiv": 21, "rational": 21, "design": [21, 26], "decis": 21, "mean": [21, 22, 26], "mainten": 22, "convent": [21, 23], "requir": [5, 6, 21, 23, 24, 26, 27], "consist": [3, 21, 23], "index": [2, 7, 21], "need": [5, 6, 9, 21, 23, 27], "addit": [21, 23], "function": [1, 16, 17, 19, 21, 23, 24, 26, 27], "idempot": 21, "work": [9, 21, 22, 23], "compon": [21, 22], "contain": [0, 2, 4, 9, 10, 11, 19, 21, 23, 25, 26], "interfac": 21, "interact": [6, 21, 22, 23, 26], "mdf": [2, 3, 9, 21, 22], "descript": [21, 22, 25], "file": [5, 6, 21, 22], "slurp": 21, "squirt": 21, "yaml": 21, "version": [0, 9, 21, 22, 24, 26], "map": [0, 10, 11, 21, 23, 27], "specif": [0, 10, 11, 21, 22, 23, 27], "api": [2, 4, 17, 21, 23], "refer": [0, 21, 23, 26, 27], "i": [0, 2, 4, 5, 6, 8, 9, 14, 21, 22, 23, 24, 25, 26, 27], "built": [9, 21, 23], "word": [21, 22, 23, 27], "therefor": [21, 23, 26], "differ": [9, 21, 22, 23], "context": [13, 15, 21, 22, 23], "confus": 21, "especi": [21, 22, 23], "sinc": [0, 21, 23], "cancer": 21, "research": 21, "common": [0, 21, 22, 24, 26], "set": [0, 2, 3, 4, 5, 6, 8, 9, 11, 13, 14, 21, 22, 23, 24, 25, 27], "up": [21, 25], "which": [0, 5, 6, 10, 11, 21, 22, 23, 24, 25, 26, 27], "central": 21, "repositori": [21, 22], "kind": [21, 22, 23, 27], "thi": [0, 2, 3, 4, 5, 6, 9, 10, 11, 19, 21, 22, 23, 24, 25, 26, 27], "relat": [14, 21, 23, 26, 27], "document": [19, 21, 22, 23, 24], "attempt": [0, 21, 27], "distinguish": [21, 22, 23, 27], "follow": [5, 6, 21, 22, 23, 24, 27], "instanc": [0, 2, 3, 4, 7, 9, 10, 11, 21, 22, 23, 26, 27], "usual": [0, 21, 24, 27], "categori": [21, 26], "item": [9, 21, 23, 27], "interest": 21, "real": 21, "world": 21, "ha": [0, 2, 8, 11, 21, 23, 26, 27], "other": [21, 22, 23, 26], "within": [9, 21, 22, 23, 27], "group": [15, 21, 22, 23], "via": [0, 5, 6, 9, 21, 22, 23, 27], "gener": [5, 6, 10, 13, 19, 21, 22, 23, 27], "engin": [21, 22, 23], "crdc": [21, 27], "part": [21, 22, 23], "icdc": [21, 22], "between": [5, 6, 10, 11, 21, 22, 23, 26, 27], "Of": 21, "cours": 21, "have": [2, 4, 5, 6, 9, 21, 22, 23, 25, 26, 27], "access": [0, 2, 4, 21, 22, 26], "setter": [21, 25, 26], "getter": 21, "exclus": 21, "thu": 21, "prop": [2, 4, 5, 6, 7, 9, 14, 21, 24, 26, 27], "arrai": [21, 27], "has_properti": [5, 6, 21, 22, 26], "its": [2, 4, 5, 6, 8, 9, 11, 21, 22, 23, 26, 27], "see": [2, 4, 9, 10, 21, 23, 26], "more": [5, 6, 21, 22, 23, 25], "detail": [21, 22, 23, 24], "modul": [2, 21], "search": [2, 7, 21, 22], "page": [19, 21], "softwar": [22, 23], "tool": [5, 6, 22, 23], "guidelin": 22, "necessari": [0, 22, 23, 24, 27], "enabl": [0, 10, 22, 23, 24], "organ": [22, 24], "stabl": [22, 23], "predict": 22, "so": [22, 23, 26, 27], "doe": [22, 23, 27], "get": [0, 2, 4, 5, 6, 9, 10, 22, 27], "lost": 22, "incorrectli": 22, "duplic": [0, 22, 25], "mutat": 22, "As": [13, 14, 15, 22], "grow": 22, "interconnect": 22, "vocabulari": [22, 23, 27], "increas": [22, 23], "databas": [0, 2, 4, 5, 6, 7, 8, 9, 10, 22, 24, 25, 26], "becom": 22, "less": 22, "amen": 22, "manual": 22, "cypher": [1, 2, 3, 5, 6, 10, 17, 19, 22], "statement": [2, 3, 4, 8, 13, 18, 22, 23], "one": [5, 6, 22, 23, 24, 27], "off": [9, 22], "script": 22, "At": [22, 23], "same": [9, 22, 23, 27], "time": [0, 22, 23], "complex": [22, 23], "util": [1, 19, 22], "valu": [0, 2, 4, 5, 6, 7, 9, 10, 11, 12, 14, 22, 23, 24, 26, 27], "long": 22, "remain": 22, "queri": [2, 4, 5, 6, 7, 8, 10, 17, 18, 22, 23, 27], "alwai": 22, "return": [0, 2, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 18, 22, 24, 27], "what": [9, 22, 23, 26], "schema": [22, 23, 27], "sai": [22, 23], "thei": [5, 6, 22, 23, 24, 26], "To": [22, 23, 24, 25, 27], "treat": 22, "dynam": [22, 23], "inform": [0, 2, 4, 22, 23, 27], "frequent": [22, 23], "chang": [0, 9, 22, 23, 25, 26, 27], "robust": [22, 23, 27], "allevi": 22, "sme": [5, 6, 22, 23], "rememb": [22, 27], "prevent": 22, "shortcut": [22, 27], "would": [22, 23], "affect": [22, 23], "outcom": 22, "standard": [22, 23, 26, 27], "expect": 22, "node": [0, 2, 4, 5, 6, 7, 9, 10, 11, 14, 22, 23, 24, 25, 26, 27], "cannot": 22, "ever": 22, "ad": [0, 5, 6, 10, 22, 23, 26], "reason": [5, 6, 22, 23], "perform": [22, 23, 26], "tune": 22, "tag": [2, 4, 11, 22, 27], "placehold": 22, "cursor": 22, "all": [0, 2, 4, 5, 6, 9, 22, 23, 26, 27], "valid": [5, 6, 22, 23, 24], "enhanc": 22, "temporari": 22, "modif": [22, 23, 27], "If": [0, 2, 3, 4, 5, 6, 8, 9, 11, 22, 23], "make": [18, 22, 23], "sens": [22, 23], "add": [5, 6, 9, 10, 22, 23, 27], "should": [2, 4, 8, 10, 22, 23, 26], "kei": [2, 4, 9, 11, 22, 23, 24, 26, 27], "question": [9, 22], "ask": [9, 22], "befor": 22, "perman": 22, "Will": 22, "break": [22, 23], "discuss": [22, 23, 24], "deprec": [0, 22, 25], "plan": 22, "facilit": [22, 23], "fix": 22, "mai": [22, 23, 24], "It": [0, 9, 22, 23, 24, 27], "critic": 22, "ahead": 22, "admin": 22, "complet": [14, 22, 23, 27], "out": [22, 24], "after": 22, "flexibl": [22, 23], "poss": 22, "non": 22, "null": 22, "nanoid": [2, 4, 5, 6, 8, 10, 22, 27], "six": 22, "charact": 22, "alphanumer": 22, "random": [2, 4, 8, 22], "identifi": [5, 6, 22, 23], "packag": [22, 24], "variou": 22, "languag": [16, 22], "e": [9, 10, 14, 22, 23, 26, 27], "g": [10, 14, 22, 23, 27], "onc": 22, "even": [22, 27], "when": [0, 6, 9, 22, 23], "remov": [0, 5, 6, 9, 10, 13, 22, 27], "plu": [22, 27], "string": [0, 2, 3, 4, 5, 6, 9, 13, 22, 23, 26, 27], "possibli": 22, "singl": [5, 6, 9, 10, 22, 23, 24, 27], "import": [5, 22, 23, 24], "through": [22, 23], "retir": 22, "serv": [22, 23, 26], "handl": [2, 4, 5, 6, 7, 9, 11, 14, 22, 23, 24, 25, 26, 27], "short": 22, "cut": 22, "simpl": [2, 4, 11, 22, 23, 24, 26, 27], "servic": 22, "st": 22, "append": 22, "id": [0, 2, 4, 5, 6, 10, 22, 23], "endpoint": [2, 4, 17, 18, 22], "must": [2, 7, 8, 9, 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\ No newline at end of file
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"property": [[27, 5, 1, "", "concept"], [27, 5, 1, "", "handle"], [27, 5, 1, "", "is_required"], [27, 5, 1, "", "item_domain"], [27, 5, 1, "", "model"], [27, 5, 1, "", "nanoid"], [27, 5, 1, "", "pattern"], [27, 5, 1, "", "units"], [27, 5, 1, "", "value_domain"], [27, 5, 1, "", "value_set"]], "tag": [[27, 5, 1, "", "key"], [27, 5, 1, "", "value"]], "term": [[27, 5, 1, "", "concept"], [27, 5, 1, "", "handle"], [27, 5, 1, "", "nanoid"], [27, 5, 1, "", "origin"], [27, 5, 1, "", "origin_definition"], [27, 5, 1, "", "origin_id"], [27, 5, 1, "", "origin_name"], [27, 5, 1, "", "origin_version"], [27, 5, 1, "", "value"]]}, "objtypes": {"0": "py:class", "1": "py:module", "2": "py:exception", "3": "py:method", "4": "py:property", "5": "py:attribute", "6": "py:function", "7": "py:data"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "module", "Python module"], "2": ["py", "exception", "Python exception"], "3": ["py", "method", "Python method"], "4": ["py", "property", "Python property"], "5": ["py", "attribute", "Python attribute"], "6": ["py", "function", "Python function"], "7": ["py", "data", "Python data"]}, "titleterms": {"load": 20, "an": [20, 27], "mdb": [2, 3, 4, 5, 6, 7, 8, 20, 21, 22, 23], "instanc": 20, "bento_meta": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 24], "metamodel": [21, 23], "databas": [21, 23, 27], "instal": 21, "content": [0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18, 21], "A": 21, "note": 21, "node": 21, "object": [11, 21, 26, 27], "properti": [21, 22], "attribut": [6, 12, 18, 21, 27], "indic": 21, "tabl": 21, "mainten": [], "principl": 23, "convent": 22, "entiti": [0, 14, 22, 23, 26], "requir": 22, "consist": 22, "index": 22, "need": 22, "addit": 22, "function": [2, 3, 4, 5, 6, 8, 11, 14, 15, 18, 22], "idempot": 22, "updat": [22, 26], "uniqu": 22, "exist": 22, "reus": 22, "semant": 22, "role": 22, "encod": 22, "map": [22, 26], "model": [9, 22, 23, 24, 25, 27], "term": [22, 27], "motiv": 23, "rational": 23, "design": 23, "decis": 23, "structur": 23, "mean": 23, "mdf": 24, "descript": 24, "file": 24, "slurp": 24, "squirt": 24, "yaml": 24, "version": 25, "us": 25, "specif": 26, "defin": 26, "subclass": 26, "ar": 26, "deriv": 26, "from": 26, "attspec": 26, "mapspec": 26, "The": 27, "work": 27, "compon": 27, "contain": 27, "access": 27, "other": 27, "interfac": 27, "manipul": 27, "interact": 27, "pattern": 22, "graph": 22, "represent": 22, "modul": [0, 3, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18], "class": [0, 2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 18], "subpackag": [1, 2, 17], "submodul": [1, 2, 5, 16, 17], "packag": [2, 5], "loader": 3, "mdb_tool": [5, 6], "searchabl": 7, "writeabl": 8, "object_map": 10, "util": [12, 13, 14, 15, 16, 17, 18], "_engin": 12, "cypher": [13, 14, 15, 16], "claus": 13, "makeq": 18, "api": 19, "refer": 19}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx": 57}, "alltitles": {"Loading an MDB instance": [[20, "loading-an-mdb-instance"]], "bento_meta and MDF": [[24, "bento-meta-and-mdf"]], "Model Description Files": [[24, "model-description-files"]], "Slurping MDF into bento_meta": [[24, "slurping-mdf-into-bento-meta"]], "Squirting a Model into MDF YAML": [[24, "squirting-a-model-into-mdf-yaml"]], "Model Versioning": [[25, "model-versioning"]], "Using Model Versioning": [[25, "using-model-versioning"]], "Object Map Specifications": [[26, "object-map-specifications"]], "Defining and Updating Objects": [[26, "defining-and-updating-objects"]], "Subclasses are derived from Entity": [[26, "subclasses-are-derived-from-entity"]], "attspec and mapspec": [[26, "attspec-and-mapspec"]], "bento_meta.entity": [[0, "module-bento_meta.entity"]], "Module Contents": [[0, "module-contents"], [3, "module-contents"], [4, "module-contents"], [6, "module-contents"], [7, "module-contents"], [8, "module-contents"], [9, "module-contents"], [10, "module-contents"], [11, "module-contents"], [12, "module-contents"], [13, "module-contents"], [14, "module-contents"], [15, "module-contents"], [18, "module-contents"]], "Classes": [[0, "classes"], [2, "classes"], [4, "classes"], [5, "classes"], [6, "classes"], [7, "classes"], [8, "classes"], [9, "classes"], [10, "classes"], [11, "classes"], [12, "classes"], [13, "classes"], [14, "classes"], [15, "classes"], [18, "classes"]], "bento_meta": [[1, "module-bento_meta"]], "Subpackages": [[1, "subpackages"], [2, "subpackages"], [17, "subpackages"]], "Submodules": [[1, "submodules"], [2, "submodules"], [5, "submodules"], [16, "submodules"], [17, "submodules"]], "bento_meta.mdb": [[2, "module-bento_meta.mdb"]], "Package Contents": [[2, "package-contents"], [5, "package-contents"]], "Functions": [[2, "functions"], [3, "functions"], [4, "functions"], [5, "functions"], [6, "functions"], [8, "functions"], [11, "functions"], [14, "functions"], [15, "functions"], [18, "functions"]], "bento_meta.mdb.loaders": [[3, "module-bento_meta.mdb.loaders"]], "bento_meta.mdb.mdb": [[4, "module-bento_meta.mdb.mdb"]], "bento_meta.mdb.mdb_tools": [[5, "module-bento_meta.mdb.mdb_tools"]], "bento_meta.mdb.mdb_tools.mdb_tools": [[6, "module-bento_meta.mdb.mdb_tools.mdb_tools"]], "Attributes": [[6, "attributes"], [12, "attributes"], [18, "attributes"]], "bento_meta.mdb.searchable": [[7, "module-bento_meta.mdb.searchable"]], "bento_meta.mdb.writeable": [[8, "module-bento_meta.mdb.writeable"]], "bento_meta.model": [[9, "module-bento_meta.model"]], "bento_meta.object_map": [[10, "module-bento_meta.object_map"]], "bento_meta.objects": [[11, "module-bento_meta.objects"]], "bento_meta.util._engine": [[12, "module-bento_meta.util._engine"]], "bento_meta.util.cypher.clauses": [[13, "module-bento_meta.util.cypher.clauses"]], "bento_meta.util.cypher.entities": [[14, "module-bento_meta.util.cypher.entities"]], "bento_meta.util.cypher.functions": [[15, "module-bento_meta.util.cypher.functions"]], "bento_meta.util.cypher": [[16, "module-bento_meta.util.cypher"]], "bento_meta.util": [[17, "module-bento_meta.util"]], "bento_meta.util.makeq": [[18, "module-bento_meta.util.makeq"]], "API Reference": [[19, "api-reference"]], "bento_meta and Metamodel Database (MDB)": [[21, "bento-meta-and-metamodel-database-mdb"]], "Installation": [[21, "installation"]], "Contents:": [[21, null]], "A Note on \u201cNodes\u201d": [[21, "a-note-on-nodes"]], "A Note on Objects, Properties, and Attributes": [[21, "a-note-on-objects-properties-and-attributes"]], "Indices and tables": [[21, "indices-and-tables"]], "MDB Conventions and Patterns": [[22, "mdb-conventions-and-patterns"]], "MDB entity properties required for consistency": [[22, "mdb-entity-properties-required-for-consistency"]], "MDB indexes needed for additional functionality": [[22, "mdb-indexes-needed-for-additional-functionality"]], "Conventions for consistent and idempotent updates": [[22, "conventions-for-consistent-and-idempotent-updates"]], "Uniqueness and Existence of Entities": [[22, "uniqueness-and-existence-of-entities"]], "Graph Patterns for Representation": [[22, "graph-patterns-for-representation"]], "\u201cReuse\u201d of Semantic Roles in MDB": [[22, "reuse-of-semantic-roles-in-mdb"]], "Encoding \u201cMappings\u201d": [[22, "encoding-mappings"]], "Models": [[22, "models"]], "Terms": [[22, "terms"]], "Metamodel Database (MDB) Principles": [[23, "metamodel-database-mdb-principles"]], "MDB Motivation and Rationale": [[23, "mdb-motivation-and-rationale"]], "MDB Design Decisions": [[23, "mdb-design-decisions"]], "MDB Entities and Structures": [[23, "mdb-entities-and-structures"]], "Models and Meanings": [[23, "models-and-meanings"]], "The Object Model": [[27, "the-object-model"]], "Working with Models": [[27, "working-with-models"]], "Component Objects": [[27, "component-objects"]], "Object attributes": [[27, "object-attributes"]], "Model as a Container": [[27, "model-as-a-container"]], "Accessing other objects": [[27, "accessing-other-objects"]], "Model as an Interface": [[27, "model-as-an-interface"]], "Manipulating Terms": [[27, "manipulating-terms"]], "Database Interaction": [[27, "database-interaction"]], "Objects and their Attributes": [[27, "objects-and-their-attributes"]]}, "indexentries": {"concept (built-in class)": [[27, "Concept"]], "edge (built-in class)": [[27, "Edge"]], "entity (built-in class)": [[27, "Entity"]], "node (built-in class)": [[27, "Node"]], "origin (built-in class)": [[27, "Origin"]], "predicate (built-in class)": [[27, "Predicate"]], "property (built-in class)": [[27, "Property"]], "tag (built-in class)": [[27, "Tag"]], "term (built-in class)": [[27, "Term"]], "_commit (entity attribute)": [[27, "entity._commit"]], "_from (entity attribute)": [[27, "entity._from"]], "_id (entity attribute)": [[27, "entity._id"]], "_next (entity attribute)": [[27, "entity._next"]], "_prev (entity attribute)": [[27, "entity._prev"]], "_to (entity attribute)": [[27, "entity._to"]], "concept (edge attribute)": [[27, "edge.concept"]], "concept (node attribute)": [[27, "node.concept"]], "concept (property attribute)": [[27, "property.concept"]], "concept (term attribute)": [[27, "term.concept"]], "desc (entity attribute)": [[27, "entity.desc"]], "dst (edge attribute)": [[27, "edge.dst"]], "handle (edge attribute)": [[27, "edge.handle"]], "handle (node attribute)": [[27, "node.handle"]], "handle (predicate attribute)": [[27, "predicate.handle"]], "handle (property attribute)": [[27, "property.handle"]], "handle (term attribute)": [[27, "term.handle"]], "is_external (origin attribute)": [[27, "origin.is_external"]], "is_required (edge attribute)": [[27, "edge.is_required"]], "is_required (property attribute)": [[27, "property.is_required"]], "item_domain (property attribute)": [[27, "property.item_domain"]], "key (tag attribute)": [[27, "tag.key"]], "model (edge attribute)": [[27, "edge.model"]], "model (node attribute)": [[27, "node.model"]], "model (property attribute)": [[27, "property.model"]], "multiplicity (edge attribute)": [[27, "edge.multiplicity"]], "name (origin attribute)": [[27, "origin.name"]], "nanoid (edge attribute)": [[27, "edge.nanoid"]], "nanoid (entity attribute)": [[27, "entity.nanoid"]], "nanoid (node attribute)": [[27, "node.nanoid"]], "nanoid (origin attribute)": [[27, "origin.nanoid"]], "nanoid (property attribute)": [[27, "property.nanoid"]], "nanoid (term attribute)": [[27, "term.nanoid"]], "object (predicate attribute)": [[27, "predicate.object"]], "origin (term attribute)": [[27, "term.origin"]], "origin_definition (term attribute)": [[27, "term.origin_definition"]], "origin_id (term attribute)": [[27, "term.origin_id"]], "origin_name (term attribute)": [[27, "term.origin_name"]], "origin_version (term attribute)": [[27, "term.origin_version"]], "pattern (property attribute)": [[27, "property.pattern"]], "props (edge attribute)": [[27, "edge.props"]], "props (node attribute)": [[27, "node.props"]], "src (edge attribute)": [[27, "edge.src"]], "subject (predicate attribute)": [[27, "predicate.subject"]], "tags (entity attribute)": [[27, "entity.tags"]], "terms (concept attribute)": [[27, "concept.terms"]], "units (property attribute)": [[27, "property.units"]], "url (origin attribute)": [[27, "origin.url"]], "value (tag attribute)": [[27, "tag.value"]], "value (term attribute)": [[27, "term.value"]], "value_domain (property attribute)": [[27, "property.value_domain"]], "value_set (property attribute)": [[27, "property.value_set"]]}})
\ No newline at end of file
diff --git a/python/docs/mdb-conventions.rst b/python/docs/mdb-conventions.rst
index d35a258..f07e7e3 100644
--- a/python/docs/mdb-conventions.rst
+++ b/python/docs/mdb-conventions.rst
@@ -81,7 +81,7 @@ _______________________________________________
For integration with the STS, and for performance, the Neo4j instance
of an MDB requires certain indexes to be established. These are
-specified in `these Cypher statements `_. The primary
+specified in `these Cypher statements `_. The primary
requirement is that fulltext, Lucene-based indexes should be created
on entity ``description`` and Term ``origin_definition`` properties to
enable "search box" like queries over the the entire graph. Regular
@@ -120,7 +120,7 @@ on `Cypher ",
diff --git a/python/src/bento_meta/mdb/mdb.py b/python/src/bento_meta/mdb/mdb.py
index 525da94..d1f8f67 100644
--- a/python/src/bento_meta/mdb/mdb.py
+++ b/python/src/bento_meta/mdb/mdb.py
@@ -244,8 +244,8 @@ def get_term_by_id(self, nanoid):
qry = (
"match (t:term {nanoid:$nanoid}) "
"where not exists(t._to) "
- "with t "
- "optional match (t)-[:has_origin]->(o:origin) "
+ "with t, t.origin_name as origin_name "
+ "optional match (o:origin {name: origin_name}) "
"where not exists(o._to) "
"return t as term, o as origin "
)
diff --git a/python/tox.ini b/python/tox.ini
index ef63d4c..7094630 100644
--- a/python/tox.ini
+++ b/python/tox.ini
@@ -7,5 +7,6 @@ deps = pytest
docker-compose
pytest-docker
commands =
- pytest
+ pytest -m "not slow"
+