From e0d2e848c6cac3ebde04445f1bc0631a7e8553d9 Mon Sep 17 00:00:00 2001 From: Quirin Manz Date: Wed, 17 Aug 2022 13:07:22 +0200 Subject: [PATCH] version 0.9 and adding diff to v0.8 --- openrefine/v0.9/create_diff_v0.9_v0.8.py | 14 + openrefine/v0.9/create_v0.9.py | 8 +- openrefine/v0.9/diff_v0.8_v0.9.json | 13669 +++++++++++++++++++++ 3 files changed, 13687 insertions(+), 4 deletions(-) create mode 100644 openrefine/v0.9/create_diff_v0.9_v0.8.py create mode 100644 openrefine/v0.9/diff_v0.8_v0.9.json diff --git a/openrefine/v0.9/create_diff_v0.9_v0.8.py b/openrefine/v0.9/create_diff_v0.9_v0.8.py new file mode 100644 index 0000000..8f69c7c --- /dev/null +++ b/openrefine/v0.9/create_diff_v0.9_v0.8.py @@ -0,0 +1,14 @@ +import os +import pandas as pd + +# make sure the working directory when running this file is the project root of the git repository +os.chdir('../../') + +old = pd.read_csv('openrefine/v0.8/IHEC_metadata_harmonization.v0.8.csv') +old.index = old.EpiRR +new = pd.read_csv('openrefine/v0.9/IHEC_metadata_harmonization.v0.9.csv') +new.index = new.EpiRR + +diff_tbl = old.compare(new) +diff_tbl.rename(columns={'self': 'v0.8', 'other': 'v0.9'}, inplace=True) +diff_tbl.apply(lambda x: [x.dropna()], axis=1).to_json('openrefine/v0.9/diff_v0.8_v0.9.json', indent=True) diff --git a/openrefine/v0.9/create_v0.9.py b/openrefine/v0.9/create_v0.9.py index 6c18c13..20acde7 100644 --- a/openrefine/v0.9/create_v0.9.py +++ b/openrefine/v0.9/create_v0.9.py @@ -1,16 +1,16 @@ -import json import os.path import warnings +import xml.etree.ElementTree as et +from collections import defaultdict from subprocess import run +from typing import Dict, List, Tuple + import pandas as pd -from collections import defaultdict # make sure the working directory when running this file is the project root of the git project os.chdir('../../') # first get the ncit thesaurus -from typing import Dict, List, Tuple -import xml.etree.ElementTree as et tree = et.parse('ontologies/Thesaurus.owl') root = tree.getroot() diff --git a/openrefine/v0.9/diff_v0.8_v0.9.json b/openrefine/v0.9/diff_v0.8_v0.9.json new file mode 100644 index 0000000..a30d379 --- /dev/null +++ b/openrefine/v0.9/diff_v0.8_v0.9.json @@ -0,0 +1,13669 @@ +{ + "IHECRE00000001.4":[ + { + "('donor_health_status_ontology_curie', 'v0.9')":"NCIM:C0678222" + } + ], + "IHECRE00000002.3":[ + { + "('donor_health_status_ontology_curie', 'v0.9')":"NCIM:C0023487", + "('disease', 'v0.8')":"Acute Promyelocytic Leukemia With Pml-rara", + "('disease', 'v0.9')":"Acute Promyelocytic Leukemia with PML-RARA" + } + ], + "IHECRE00000003.3":[ + { + "('disease_ontology_curie', 'v0.9')":"NCIM:C0549184" + } + ], + "IHECRE00000004.3":[ + { + "('disease_ontology_curie', 'v0.9')":"NCIM:C0549184" + } + ], + "IHECRE00000006.3":[ + { + "('disease_ontology_curie', 'v0.9')":"NCIM:C0549184" + } + ], + "IHECRE00000008.3":[ + { + "('disease_ontology_curie', 'v0.9')":"NCIM:C0549184" + } + ], + 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