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Update release to merged axiom annotations
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@matentzn
matentzn committed Apr 5, 2024
1 parent c8c3642 commit 5b9ba37
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Showing 2 changed files with 47 additions and 21 deletions.
9 changes: 9 additions & 0 deletions src/ontology/vbo.Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -93,3 +93,12 @@ dadis-local-sync: $(COMPONENTSDIR)/dadisbreedcountry.owl

.PHONY: dadistransbound
dadis-transboundary-sync: $(COMPONENTSDIR)/dadistransbound.owl

###########################################
##### Release preprocessing ###############
###########################################

$(EDIT_PREPROCESSED): $(SRC)
$(ROBOT) merge --input $< --output $@.merged.owl
owltools --use-catalog $@.merged.owl --merge-axiom-annotations -o -f owl $@.normalised.owl
$(ROBOT) convert --input $@.normalised.owl --format ofn --output $@
59 changes: 38 additions & 21 deletions src/scripts/dadis_client/vbo_sandbox.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
Expand All @@ -19,24 +19,9 @@
},
{
"cell_type": "code",
"execution_count": 31,
"execution_count": 3,
"metadata": {},
"outputs": [
{
"ename": "KeyError",
"evalue": "\"['obsolesence_reason'] not in index\"",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mKeyError\u001b[0m Traceback (most recent call last)",
"Cell \u001b[0;32mIn[31], line 42\u001b[0m\n\u001b[1;32m 40\u001b[0m out \u001b[38;5;241m=\u001b[39m merge(df, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mVBO:0200238\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mVBO:0200239\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 41\u001b[0m out\u001b[38;5;241m.\u001b[39mto_csv(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdogbreeds_merged.tsv\u001b[39m\u001b[38;5;124m\"\u001b[39m,sep\u001b[38;5;241m=\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;130;01m\\t\u001b[39;00m\u001b[38;5;124m\"\u001b[39m,index\u001b[38;5;241m=\u001b[39m\u001b[38;5;28;01mFalse\u001b[39;00m)\n\u001b[0;32m---> 42\u001b[0m \u001b[43mout\u001b[49m\u001b[43m[\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mobsolesence_reason\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mobsolete\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mterm_label\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mvbo_id\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mreplacement_term\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mreplacement_label\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mGH_issue\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mobsoletion_type\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43mcontributors\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msynonym_label_from_merged_term\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msource_for_merged_term\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m,\u001b[49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[38;5;124;43msynonym_type_most_common_name\u001b[39;49m\u001b[38;5;124;43m'\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m]\u001b[49m\n",
"File \u001b[0;32m~/.pyenv/versions/3.11.7/envs/grainyhead/lib/python3.11/site-packages/pandas/core/frame.py:4096\u001b[0m, in \u001b[0;36mDataFrame.__getitem__\u001b[0;34m(self, key)\u001b[0m\n\u001b[1;32m 4094\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m is_iterator(key):\n\u001b[1;32m 4095\u001b[0m key \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(key)\n\u001b[0;32m-> 4096\u001b[0m indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcolumns\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_get_indexer_strict\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkey\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43mcolumns\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m)\u001b[49m[\u001b[38;5;241m1\u001b[39m]\n\u001b[1;32m 4098\u001b[0m \u001b[38;5;66;03m# take() does not accept boolean indexers\u001b[39;00m\n\u001b[1;32m 4099\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mgetattr\u001b[39m(indexer, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mdtype\u001b[39m\u001b[38;5;124m\"\u001b[39m, \u001b[38;5;28;01mNone\u001b[39;00m) \u001b[38;5;241m==\u001b[39m \u001b[38;5;28mbool\u001b[39m:\n",
"File \u001b[0;32m~/.pyenv/versions/3.11.7/envs/grainyhead/lib/python3.11/site-packages/pandas/core/indexes/base.py:6200\u001b[0m, in \u001b[0;36mIndex._get_indexer_strict\u001b[0;34m(self, key, axis_name)\u001b[0m\n\u001b[1;32m 6197\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[1;32m 6198\u001b[0m keyarr, indexer, new_indexer \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_reindex_non_unique(keyarr)\n\u001b[0;32m-> 6200\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_raise_if_missing\u001b[49m\u001b[43m(\u001b[49m\u001b[43mkeyarr\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mindexer\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43maxis_name\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 6202\u001b[0m keyarr \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mtake(indexer)\n\u001b[1;32m 6203\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28misinstance\u001b[39m(key, Index):\n\u001b[1;32m 6204\u001b[0m \u001b[38;5;66;03m# GH 42790 - Preserve name from an Index\u001b[39;00m\n",
"File \u001b[0;32m~/.pyenv/versions/3.11.7/envs/grainyhead/lib/python3.11/site-packages/pandas/core/indexes/base.py:6252\u001b[0m, in \u001b[0;36mIndex._raise_if_missing\u001b[0;34m(self, key, indexer, axis_name)\u001b[0m\n\u001b[1;32m 6249\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mNone of [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mkey\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m] are in the [\u001b[39m\u001b[38;5;132;01m{\u001b[39;00maxis_name\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 6251\u001b[0m not_found \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mlist\u001b[39m(ensure_index(key)[missing_mask\u001b[38;5;241m.\u001b[39mnonzero()[\u001b[38;5;241m0\u001b[39m]]\u001b[38;5;241m.\u001b[39munique())\n\u001b[0;32m-> 6252\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m \u001b[38;5;167;01mKeyError\u001b[39;00m(\u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00mnot_found\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m not in index\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n",
"\u001b[0;31mKeyError\u001b[0m: \"['obsolesence_reason'] not in index\""
]
}
],
"outputs": [],
"source": [
"def merge(df, term_to_obsolete, term_to_merge_into, issue=1):\n",
" df_term_to_merge_into = df[df[\"vbo_id\"]==term_to_merge_into].copy()\n",
Expand Down Expand Up @@ -70,9 +55,41 @@
"\n",
" return pd.concat([df_term_to_obsolete, df_term_to_obsolete2, df_term_to_merge_into])\n",
"\n",
"df=pd.read_csv(template_url,sep=\"\\t\")\n",
"out = merge(df, term_to_obsolete, term_to_merge_into,issue=issue)\n",
"out.to_csv(outfile,sep=\"\\t\",index=False)\n"
"\n",
"def obsolete_and_write(template_url, term_to_obsolete, term_to_merge_into, issue, outfile):\n",
" df=pd.read_csv(template_url,sep=\"\\t\")\n",
" out = merge(df, term_to_obsolete, term_to_merge_into,issue=issue)\n",
" out.to_csv(outfile,sep=\"\\t\",index=False)\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"obsolete_and_write(template_url=\"dogbreeds_merged.tsv\",\n",
" template_url=\"https://docs.google.com/spreadsheets/d/e/2PACX-1vSuwLXikgq08frK7d8yFSdWTS8P1erx5bS_QiLdHhfKV4ulJlRrqkVaVhC7b3O6Z8ixrvJgoCBy8YLq/pub?gid=1655315858&single=true&output=tsv\",\n",
" term_to_obsolete = \"VBO:0200238\",\n",
" term_to_merge_into = \"VBO:0200239\",\n",
" issue = 123,\n",
" outfile = \"dogbreeds_merged.tsv\"\n",
")\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"obsolete_and_write(template_url=\"dogbreeds_merged.tsv\",\n",
" template_url=\"https://docs.google.com/spreadsheets/d/e/2PACX-1vSuwLXikgq08frK7d8yFSdWTS8P1erx5bS_QiLdHhfKV4ulJlRrqkVaVhC7b3O6Z8ixrvJgoCBy8YLq/pub?gid=1655315858&single=true&output=tsv\",\n",
" term_to_obsolete = \"VBO:0200238\",\n",
" term_to_merge_into = \"VBO:0200239\",\n",
" issue = 123,\n",
" outfile = \"dogbreeds_merged.tsv\"\n",
")"
]
}
],
Expand Down

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