kraph 0.2.0__tar.gz → 0.3.0__tar.gz

kraph-0.3.0/.gitignore

@@ -0,0 +1,147 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+**/__pycache__
+*.py[cod]
+*$py.class
+*.pyc
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# static files generated from Django application using `collectstatic`
+media
+export
+static_collected
+data

kraph-0.3.0/PKG-INFO

@@ -0,0 +1,29 @@
+Metadata-Version: 2.4
+Name: kraph
+Version: 0.3.0
+Summary: the arkitekt knowledge graph
+Author-email: jhnnsrs <jhnnsrs@gmail.com>
+License-Expression: GPL-3.0-or-later
+Requires-Python: <4.0,>=3.11
+Requires-Dist: dokker>=2.3
+Requires-Dist: rath>=3.5
+Requires-Dist: websockets>=15.0.1
+Description-Content-Type: text/markdown
+
+# kraph
+
+Kraph is a Python library for creating and manipulating knowledge graphs build around apache AGE. 
+
+## Features
+
+- Create and manipulate knowledge graphs
+- Query knowledge graphs using Cypher
+- Ontology support (custom entities and relationships)
+- GraphQL API for adding and querying data
+
+
+## Installation
+
+```bash
+pip install kraph
+```

kraph-0.3.0/README.md

@@ -0,0 +1,17 @@
+# kraph
+
+Kraph is a Python library for creating and manipulating knowledge graphs build around apache AGE. 
+
+## Features
+
+- Create and manipulate knowledge graphs
+- Query knowledge graphs using Cypher
+- Ontology support (custom entities and relationships)
+- GraphQL API for adding and querying data
+
+
+## Installation
+
+```bash
+pip install kraph
+```

kraph-0.3.0/kraph/__init__.py

@@ -0,0 +1,23 @@
+from .kraph import Kraph
+
+
+try:
+    from .arkitekt import KraphService
+except ImportError as e:
+    try:
+        import arkitekt_next
+    except ImportError:
+        pass
+    else:
+        raise e
+try:
+    from .rekuest import structure_reg
+except ImportError as e:
+    try:
+        import rekuest_next
+    except ImportError:
+        pass
+    else:
+        raise e
+
+__all__ = ["Kraph", "structure_reg", "KraphService"]

{kraph-0.2.0 → kraph-0.3.0}/kraph/api/project.json

@@ -84,6 +84,12 @@
                 "Graph": [
                     "kraph.traits.GraphTrait"
                 ],
+                "Node": [
+                    "kraph.traits.NodeTrait"
+                ],
+                "NodeCategory": [
+                    "kraph.traits.NodeCategoryTrait"
+                ],
                 "StructureCategory": [
                     "kraph.traits.StructureCategoryTrait"
                 ],
@@ -108,6 +114,9 @@
                 "RelationCategory": [
                     "kraph.traits.RelationCategoryTrait"
                 ],
+                "StructureRelationCategory": [
+                    "kraph.traits.StructureRelationCategoryTrait"
+                ],
                 "EntityRoleDefinitionInput": [
                     "kraph.traits.EntityRoleDefinitionInputTrait"
                 ],
@@ -132,6 +141,9 @@
                 "RelationCategoryInput": [
                     "kraph.traits.RelationCategoryInputTrait"
                 ],
+                "StructureRelationCategoryInput": [
+                    "kraph.traits.StructureRelationCategoryInputTrait"
+                ],
                 "MeasurementCategoryInput": [
                     "kraph.traits.MeasurementCategoryInputTrait"
                 ],
@@ -157,6 +169,11 @@
                 },
                 {
                     "type": "turms.plugins.funcs.FuncsPlugin",
+                    "coercible_scalars": {
+                        "ID": "rath.scalars.IDCoercible",
+                        "Cypher": "kraph.scalars.CypherCoercible",
+                        "StructureIdentifier": "kraph.scalars.StructureIdentifierCoercible"
+                    },
                     "expand_input_types": [
                         "input"
                     ],

{kraph-0.2.0 → kraph-0.3.0}/kraph/api/schema.graphql

@@ -1,11 +1,3 @@
-"""Make string uppercase"""
-directive @upper on FIELD
-
-directive @replace(old: String!, new: String!) on FIELD
-
-"""Make get stuff uppercase"""
-directive @relation(on: String!) on FIELD
-
 """
 A Entity is a recorded data point in a graph. It can measure a property of an entity through a direct measurement edge, that connects the entity to the structure. It of course can relate to other structures through relation edges.
 """
@@ -108,6 +100,9 @@ type Graph {
 
   """The list of relation expressions defined in this ontology"""
   relationCategories(filters: RelationCategoryFilter, pagination: OffsetPaginationInput): [RelationCategory!]!
+
+  """The list of structure relation expressions defined in this ontology"""
+  structureRelationCategories(filters: StructureRelationCategoryFilter, pagination: OffsetPaginationInput): [StructureRelationCategory!]!
   nodeCategories(filters: NodeCategoryFilter, pagination: OffsetPaginationInput): [NodeCategory!]!
   edgeCategories(filters: EdgeCategoryFilter, pagination: OffsetPaginationInput): [EdgeCategory!]!
   latestNodes(filters: EntityFilter = null, pagination: GraphPaginationInput = null): [Node!]!
@@ -123,11 +118,13 @@ input NodeQueryFilter {
   id: ID
   AND: NodeQueryFilter
   OR: NodeQueryFilter
+  NOT: NodeQueryFilter
+  DISTINCT: Boolean
 }
 
 input OffsetPaginationInput {
   offset: Int! = 0
-  limit: Int! = -1
+  limit: Int
 }
 
 """A view of a graph, that contains entities and relations."""
@@ -172,6 +169,8 @@ input ScatterPlotFilter {
   id: ID
   AND: ScatterPlotFilter
   OR: ScatterPlotFilter
+  NOT: ScatterPlotFilter
+  DISTINCT: Boolean
 }
 
 union PathPairsTable = Path | Pairs | Table
@@ -193,10 +192,10 @@ type Pairs {
 """A paired structure two entities and the relation between them."""
 type Pair {
   """The left entity."""
-  left: Node!
+  source: Node!
 
   """The right entity."""
-  right: Node!
+  target: Node!
 
   """The relation between the two entities."""
   edge: Edge!
@@ -259,6 +258,8 @@ input GraphQueryFilter {
   id: ID
   AND: GraphQueryFilter
   OR: GraphQueryFilter
+  NOT: GraphQueryFilter
+  DISTINCT: Boolean
 }
 
 type MetricCategory implements NodeCategory & BaseCategory {
@@ -417,6 +418,8 @@ input TagFilter {
   values: [String!] = null
   AND: TagFilter
   OR: TagFilter
+  NOT: TagFilter
+  DISTINCT: Boolean
 }
 
 type StructureCategoryDefinition implements CategoryDefintion {
@@ -495,6 +498,8 @@ input MetricCategoryFilter {
   pinned: Boolean
   AND: MetricCategoryFilter
   OR: MetricCategoryFilter
+  NOT: MetricCategoryFilter
+  DISTINCT: Boolean
 }
 
 input StructureCategoryFilter {
@@ -506,6 +511,8 @@ input StructureCategoryFilter {
   pinned: Boolean
   AND: StructureCategoryFilter
   OR: StructureCategoryFilter
+  NOT: StructureCategoryFilter
+  DISTINCT: Boolean
 }
 
 type ProtocolEventCategory implements NodeCategory & BaseCategory {
@@ -761,6 +768,8 @@ input ProtocolEventCategoryFilter {
   pinned: Boolean
   AND: ProtocolEventCategoryFilter
   OR: ProtocolEventCategoryFilter
+  NOT: ProtocolEventCategoryFilter
+  DISTINCT: Boolean
 }
 
 type NaturalEventCategory implements NodeCategory & BaseCategory {
@@ -833,6 +842,8 @@ input NaturalEventCategoryFilter {
   pinned: Boolean
   AND: NaturalEventCategoryFilter
   OR: NaturalEventCategoryFilter
+  NOT: NaturalEventCategoryFilter
+  DISTINCT: Boolean
 }
 
 input EntityCategoryFilter {
@@ -845,6 +856,8 @@ input EntityCategoryFilter {
   tags: [String!]
   AND: EntityCategoryFilter
   OR: EntityCategoryFilter
+  NOT: EntityCategoryFilter
+  DISTINCT: Boolean
 }
 
 input ReagentCategoryFilter {
@@ -856,6 +869,8 @@ input ReagentCategoryFilter {
   pinned: Boolean
   AND: ReagentCategoryFilter
   OR: ReagentCategoryFilter
+  NOT: ReagentCategoryFilter
+  DISTINCT: Boolean
 }
 
 type MeasurementCategory implements EdgeCategory & BaseCategory {
@@ -913,6 +928,8 @@ input MeasurementCategoryFilter {
   graph: ID
   AND: MeasurementCategoryFilter
   OR: MeasurementCategoryFilter
+  NOT: MeasurementCategoryFilter
+  DISTINCT: Boolean
 }
 
 type RelationCategory implements EdgeCategory & BaseCategory {
@@ -967,6 +984,66 @@ input RelationCategoryFilter {
   pinned: Boolean
   AND: RelationCategoryFilter
   OR: RelationCategoryFilter
+  NOT: RelationCategoryFilter
+  DISTINCT: Boolean
+}
+
+type StructureRelationCategory implements EdgeCategory & BaseCategory {
+  """The unique identifier of the expression within its graph"""
+  id: ID!
+
+  """The ontology the expression belongs to."""
+  graph: Graph!
+
+  """A description of the expression."""
+  description: String
+
+  """
+  An image or other media file that can be used to represent the expression.
+  """
+  store: MediaStore
+
+  """The unique identifier of the expression within its graph"""
+  ageName: String!
+  color: [Float!]
+
+  """The kind of expression"""
+  kind: ExpressionKind!
+
+  """The tags that are associated with the expression"""
+  tags(filters: TagFilter, pagination: OffsetPaginationInput): [Tag!]!
+
+  """The unique identifier of the expression within its graph"""
+  purl: String
+
+  """The sequence of the expression within its graph"""
+  sequence: GraphSequence
+  relevantQueries: [GraphQuery!]!
+  relevantNodeQueries: [NodeQuery!]!
+  bestQuery: GraphQuery
+  pinned: Boolean!
+
+  """The label of the expression"""
+  label: String!
+
+  """The unique identifier of the expression within its graph"""
+  sourceDefinition: StructureCategoryDefinition!
+  targetDefinition: StructureCategoryDefinition!
+}
+
+input StructureRelationCategoryFilter {
+  ids: [ID!]
+  id: ID
+  search: String
+  graph: ID
+  ontology: ID
+  pinned: Boolean
+  sourceIdentifier: String = null
+  targetIdentifier: String = null
+  AND: StructureRelationCategoryFilter
+  OR: StructureRelationCategoryFilter
+  NOT: StructureRelationCategoryFilter
+  DISTINCT: Boolean
 }
 
 input NodeCategoryFilter {
@@ -1452,6 +1529,9 @@ type Query {
   """List of all measurement categories"""
   measurementCategories(filters: MeasurementCategoryFilter, pagination: OffsetPaginationInput): [MeasurementCategory!]!
 
+  """List of all structure relation categories"""
+  structureRelationCategories(filters: StructureRelationCategoryFilter, pagination: OffsetPaginationInput): [StructureRelationCategory!]!
+
   """List of all scatter plots"""
   scatterPlots(filters: ScatterPlotFilter, pagination: OffsetPaginationInput): [ScatterPlot!]!
 
@@ -1478,6 +1558,7 @@ type Query {
   graphSequence(id: ID!): GraphSequence!
   entityCategory(id: ID!): EntityCategory!
   getEntityByCategoryAndExternalId(category: ID!, externalId: String!): Entity!
+  structureRelationCategory(id: ID!): StructureRelationCategory!
   metricCategory(id: ID!): MetricCategory!
   structureCategory(id: ID!): StructureCategory!
   naturalEventCategory(id: ID!): NaturalEventCategory!
@@ -1524,6 +1605,8 @@ input GraphFilter {
   pinned: Boolean = null
   AND: GraphFilter
   OR: GraphFilter
+  NOT: GraphFilter
+  DISTINCT: Boolean
 }
 
 input GraphSequenceFilter {
@@ -1535,6 +1618,8 @@ input GraphSequenceFilter {
   id: ID
   AND: GraphSequenceFilter
   OR: GraphSequenceFilter
+  NOT: GraphSequenceFilter
+  DISTINCT: Boolean
 }
 
 """
@@ -1558,6 +1643,8 @@ input ModelFilter {
   search: String
   AND: ModelFilter
   OR: ModelFilter
+  NOT: ModelFilter
+  DISTINCT: Boolean
 }
 
 """Filter for entity relations in the graph"""
@@ -1813,6 +1900,15 @@ type Mutation {
   """Delete an existing expression"""
   deleteRelationCategory(input: DeleteRelationCategoryInput!): ID!
 
+  """Create a new expression"""
+  createStructureRelationCategory(input: StructureRelationCategoryInput!): StructureRelationCategory!
+
+  """Update an existing expression"""
+  updateStructureRelationCategory(input: UpdateStructureRelationCategoryInput!): StructureRelationCategory!
+
+  """Delete an existing expression"""
+  deleteStructureRelationCategory(input: DeleteStructureRelationCategoryInput!): ID!
+
   """Create a new expression"""
   createEntityCategory(input: EntityCategoryInput!): EntityCategory!
 
@@ -1873,6 +1969,9 @@ type Mutation {
   """Create a new relation between entities"""
   createRelation(input: RelationInput!): Relation!
 
+  """Create a new relation between entities"""
+  createStructureRelation(input: StructureRelationInput!): StructureRelation!
+
   """Create a new metric for an entity"""
   createMetric(input: MetricInput!): Metric!
 
@@ -2314,6 +2413,99 @@ input DeleteRelationCategoryInput {
   id: ID!
 }
 
+"""Input for creating a new expression"""
+input StructureRelationCategoryInput {
+  """
+  The ID of the graph this expression belongs to. If not provided, uses default ontology
+  """
+  graph: ID!
+
+  """A detailed description of the expression"""
+  description: String = null
+
+  """Permanent URL identifier for the expression"""
+  purl: String = null
+
+  """RGBA color values as list of 3 or 4 integers"""
+  color: [Int!] = null
+
+  """An optional image associated with this expression"""
+  image: ID = null
+
+  """A list of tags associated with this expression"""
+  tags: [String!] = null
+
+  """Whether this expression should be pinned or not"""
+  pin: Boolean = null
+
+  """The ID of the sequence this category will get internal_ids from"""
+  sequence: ID = null
+
+  """Whether to create a sequence if it does not exist"""
+  autoCreateSequence: Boolean = false
+
+  """The label/name of the expression"""
+  label: String!
+
+  """The source definition for this expression"""
+  sourceDefinition: StructureCategoryDefinitionInput!
+
+  """The target definition for this expression"""
+  targetDefinition: StructureCategoryDefinitionInput!
+}
+
+"""Input for creating a new expression"""
+input StructureCategoryDefinitionInput {
+  """A list of classes to filter the entities"""
+  categoryFilters: [ID!] = null
+
+  """A list of StructureIdentifier to filter the entities"""
+  identifierFilters: [StructureIdentifier!] = null
+
+  """A list of tags to filter the entities by"""
+  tagFilters: [String!] = null
+
+  """
+  The default ACTIVE reagent to use for this port if a reagent is not provided
+  """
+  defaultUseActive: ID = null
+
+  """
+  The default creation of entity or reagent to use for this port if a reagent is not provided
+  """
+  defaultUseNew: ID = null
+}
+
+"""Input for updating an existing expression"""
+input UpdateStructureRelationCategoryInput {
+  """A detailed description of the expression"""
+  description: String = null
+
+  """Permanent URL identifier for the expression"""
+  purl: String = null
+
+  """RGBA color values as list of 3 or 4 integers"""
+  color: [Int!] = null
+
+  """An optional image associated with this expression"""
+  image: ID = null
+
+  """A list of tags associated with this expression"""
+  tags: [String!] = null
+
+  """Whether this expression should be pinned or not"""
+  pin: Boolean = null
+
+  """New label for the expression"""
+  label: String = null
+}
+
+"""Input for deleting an expression"""
+input DeleteStructureRelationCategoryInput {
+  """The ID of the expression to delete"""
+  id: ID!
+}
+
 """Input for creating a new expression"""
 input EntityCategoryInput {
   """
@@ -2976,6 +3168,42 @@ input RelationInput {
   context: ContextInput = null
 }
 
+"A relation is an edge between two entities. It is a directed edge, that connects two entities and established a relationship\n                 that is not a measurement between them. I.e. when they are an subjective assertion about the entities.\n                 \n                 \n                 \n                 "
+type StructureRelation implements Edge {
+  """The unique identifier of the entity within its graph"""
+  id: NodeID!
+  label: String!
+  leftId: String!
+  rightId: String!
+  right: Node!
+  left: Node!
+
+  """Timestamp from when this entity is valid"""
+  validFrom: DateTime!
+
+  """Timestamp until when this entity is valid"""
+  validTo: DateTime!
+
+  """When this entity was created"""
+  createdAt: DateTime!
+  category: StructureRelationCategory!
+}
+
+"""Input type for creating a relation between two entities"""
+input StructureRelationInput {
+  """ID of the left entity (format: graph:id)"""
+  source: ID!
+
+  """ID of the right entity (format: graph:id)"""
+  target: ID!
+
+  """ID of the relation category (LinkedExpression)"""
+  category: ID!
+
+  """The context of the measurement"""
+  context: ContextInput = null
+}
+
 input MetricInput {
   structure: NodeID!
   category: ID!