From 690971a9339f64b08a3b462aa0ff4ec9cc436f20 Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Wed, 15 Mar 2023 11:24:23 -0400 Subject: [PATCH 1/4] Update poetry lock --- poetry.lock | 3567 +++++++++++++++++++++++++++------------------------ 1 file changed, 1859 insertions(+), 1708 deletions(-) diff --git a/poetry.lock b/poetry.lock index 82edb42e..002c88f3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,43 +1,33 @@ -# This file is automatically @generated by Poetry and should not be changed by hand. - [[package]] name = "aiohttp" -version = "2.3.10" +version = "3.8.4" description = "Async http client/server framework (asyncio)" category = "main" optional = false -python-versions = ">=3.4.2" -files = [ - {file = "aiohttp-2.3.10-cp34-cp34m-macosx_10_10_x86_64.whl", hash = "sha256:834f687b806fbf49cb135b5a208b5c27338e19c219d6e09e9049936e01e8bea8"}, - {file = "aiohttp-2.3.10-cp34-cp34m-macosx_10_11_x86_64.whl", hash = "sha256:6b8c5a00432b8a5a083792006e8fdfb558b8b10019ce254200855264d3a25895"}, - 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b/kgx/utils/infores.py @@ -5,7 +5,6 @@ from typing import Optional, Tuple, Callable, Dict, List, Any from kgx.utils.kgx_utils import knowledge_provenance_properties, column_types -from kgx.error_detection import ErrorType, MessageLevel from kgx.config import get_logger log = get_logger() @@ -134,7 +133,7 @@ def _get_infores(source: str) -> str: def _process_infores(source: str) -> str: """ - Process a single knowledge Source name string into an infores, by applying rules + Process a single knowledge Source name string into an infores, by applying rules in the _infores_processor() closure context, followed by standard formatting. Parameters @@ -430,8 +429,9 @@ def set_node_provenance(self, node_data: Dict): def set_edge_provenance(self, edge_data: Dict): """ - Sets the edge knowledge_source value for the current edge. Edge knowledge_source properties - include the 'knowledge_source' related properties. + Sets the edge knowledge_source value for the current edge. + Edge knowledge_source properties include the + 'knowledge_source' related properties. Parameters ---------- From 1f11355c379ae95fedeb2022e652e85c29d62ea3 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 3 May 2023 14:19:11 -0700 Subject: [PATCH 3/4] add full infores map from toolkit --- kgx/source/json_source.py | 12 +----------- kgx/transformer.py | 9 ++++++++- 2 files changed, 9 insertions(+), 12 deletions(-) diff --git a/kgx/source/json_source.py b/kgx/source/json_source.py index 9179399d..3d9ce1be 100644 --- a/kgx/source/json_source.py +++ b/kgx/source/json_source.py @@ -1,19 +1,9 @@ import gzip import typing -from typing import Optional, Generator, Any import ijson from itertools import chain -from typing import Dict, Tuple, Any, Generator, Optional, List +from typing import Any, Generator, Optional from kgx.config import get_logger -from kgx.error_detection import ErrorType, MessageLevel -from kgx.source.source import Source -from kgx.utils.kgx_utils import ( - generate_uuid, - generate_edge_key, - extension_types, - archive_read_mode, - sanitize_import -) from kgx.source.tsv_source import TsvSource log = get_logger() diff --git a/kgx/transformer.py b/kgx/transformer.py index 7bce847e..e2e93dab 100644 --- a/kgx/transformer.py +++ b/kgx/transformer.py @@ -3,9 +3,10 @@ from os.path import exists from sys import stderr from typing import Dict, Generator, List, Optional, Callable, Set - +from bmt import Toolkit from kgx.config import get_logger from kgx.error_detection import ErrorType, MessageLevel, ErrorDetecting +from pprint import pprint from kgx.source import ( GraphSource, Source, @@ -110,6 +111,8 @@ def __init__( self._seen_nodes = set() self._infores_catalog: Dict[str, str] = dict() + self.toolkit = Toolkit() + if infores_catalog and exists(infores_catalog): with open(infores_catalog, "r") as irc: for entry in irc: @@ -118,6 +121,10 @@ def __init__( if entry: source, infores = entry.split("\t") self._infores_catalog[source] = infores + for k, v in self.toolkit.infores_map.items(): + self._infores_catalog[k] = v.get("name") + pprint(self._infores_catalog) + def transform( self, From e62146e77f8b6e134729641ef131ec785cd55472 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Wed, 3 May 2023 14:22:49 -0700 Subject: [PATCH 4/4] remove debugging --- kgx/transformer.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/kgx/transformer.py b/kgx/transformer.py index e2e93dab..5c1fa37e 100644 --- a/kgx/transformer.py +++ b/kgx/transformer.py @@ -122,9 +122,10 @@ def __init__( source, infores = entry.split("\t") self._infores_catalog[source] = infores for k, v in self.toolkit.infores_map.items(): - self._infores_catalog[k] = v.get("name") - pprint(self._infores_catalog) - + self._infores_catalog[k] = v.get("name").strip() + else: + for k, v in self.toolkit.infores_map.items(): + self._infores_catalog[k] = v.get("name").strip() def transform( self,