diff --git a/notebooks/Commands/ValidateMappings.ipynb b/notebooks/Commands/ValidateMappings.ipynb new file mode 100644 index 000000000..600781d82 --- /dev/null +++ b/notebooks/Commands/ValidateMappings.ipynb @@ -0,0 +1,1195 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "id": "0a28b88d-4deb-4d0a-a110-f27adf077e23", + "metadata": {}, + "source": [ + "# OAK apply command\n", + "\n", + "This notebook is intended as a supplement to the [main OAK CLI docs](https://incatools.github.io/ontology-access-kit/cli.html).\n", + "\n", + "This notebook provides examples for the `validate-mappings` command.\n", + "This forms part of a suite of *validate* commands.\n", + " \n", + "## Help Option\n", + "\n", + "You can get help on any OAK command using `--help`" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "id": "c223f678-f82f-4b06-8e19-1a5b7323e571", + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Usage: runoak validate-mappings [OPTIONS] [TERMS]...\n", + "\n", + " Validates mappings in ontology using additional ontologies.\n", + "\n", + " To run:\n", + "\n", + " runoak validate-mappings -i db/uberon.db\n", + "\n", + " For sssom:\n", + "\n", + " runoak validate-mappings -i db/uberon.db -o bad-mappings.sssom.tsv\n", + "\n", + " By default this will attempt to download and connect to sqlite versions of\n", + " different ontologies.\n", + "\n", + " You can customize this:\n", + "\n", + " runoak validate-mappings -i db/uberon.db --adapter-mapping\n", + " uberon=db/uberon.db --adapter-mapping zfa=db/zfa.db\n", + "\n", + " You can use \"*\" as a wildcard, in the case where you have an application\n", + " ontology with many mapped entities merged in:\n", + "\n", + " runoak validate-mappings -i db/uberon.db --adapter-mapping\n", + " \"*\"=db/merged.db\"\n", + "\n", + "Options:\n", + " --autolabel / --no-autolabel If set, results will automatically have labels\n", + " assigned [default: autolabel]\n", + " -O, --output-type TEXT Desired output type\n", + " --adapter-mapping TEXT Multiple prefix=selector pairs, e.g.\n", + " --adapter-mapping uberon=db/uberon.db\n", + " -o, --output FILENAME Output file, e.g. obo file\n", + " --help Show this message and exit.\n" + ] + } + ], + "source": [ + "!runoak validate-mappings --help" + ] + }, + { + "cell_type": "markdown", + "id": "01f38163-db22-4c51-ae46-10e8b8e6d53c", + "metadata": {}, + "source": [ + "## Example: Validate mappings in XAO\n", + "\n", + "XAO is an anatomical ontology for *Xenopus*. It has mappings to ontologies like UBERON, GO, CL" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "id": "c9b86e52-87a7-449c-baac-81981e7ce632", + "metadata": {}, + "outputs": [], + "source": [ + "!runoak -i sqlite:obo:xao validate-mappings -O sssom -o output/xao-invalid.sssom.tsv" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "id": "5fc9b15d-cc81-400a-8660-f92491baa120", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subject_idsubject_labelpredicate_idobject_idobject_labelmapping_justificationsubject_sourceobject_sourcemapping_cardinalitycomment
0XAO:0000054trunk regionoio:hasDbXrefUBERON:0002100trunksemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
1XAO:0000100cardiovascular systemoio:hasDbXrefUBERON:0004535cardiovascular systemsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
2XAO:0000204peripheral nerveoio:hasDbXrefUBERON:0002003obsolete peripheral nervesemapv:UnspecifiedMatchingXAOUBERON1:1object is obsolete
3XAO:0000227eye primordiumoio:hasDbXrefUBERON:0003071eye primordiumsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
4XAO:0000282visceral pouchoio:hasDbXrefUBERON:0004117pharyngeal pouchsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
5XAO:0000376omphalomesenteric veinoio:hasDbXrefUBERON:0005487vitelline veinsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
6XAO:0000427gasserian ganglionoio:hasDbXrefUBERON:0001675trigeminal ganglionsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
7XAO:0000428trigeminal ganglionoio:hasDbXrefUBERON:0001675trigeminal ganglionsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
8XAO:0001010circulatory systemoio:hasDbXrefUBERON:0004535cardiovascular systemsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
9XAO:0003001anatomical groupoio:hasDbXrefCARO:0000054anatomical groupsemapv:UnspecifiedMatchingXAOCARO1:1object is obsolete
10XAO:0003012celloio:hasDbXrefGO:0005623obsolete cellsemapv:UnspecifiedMatchingXAOGO1:1object is obsolete
11XAO:0003025trunkoio:hasDbXrefUBERON:0002100trunksemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
12XAO:0003160anatomical clusteroio:hasDbXrefCARO:0000041anatomical clustersemapv:UnspecifiedMatchingXAOCARO1:1object is obsolete
13XAO:0003163basal laminaoio:hasDbXrefCARO:0000065basal laminasemapv:UnspecifiedMatchingXAOCARO1:1object is obsolete
14XAO:0003257myelin accumulating celloio:hasDbXrefCL:0000328obsolete myelin accumulating cellsemapv:UnspecifiedMatchingXAOCL1:1object is obsolete
15XAO:0004090optic fieldoio:hasDbXrefUBERON:0003071eye primordiumsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
16XAO:0004147vitelline veinoio:hasDbXrefUBERON:0005487vitelline veinsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
17XAO:0004165intersomitic arteryoio:hasDbXrefUBERON:0006001NaNsemapv:UnspecifiedMatchingXAOUBERON1:1object is obsolete
18XAO:0004260pharyngeal pouchoio:hasDbXrefUBERON:0004117pharyngeal pouchsemapv:UnspecifiedMatchingXAOUBERON1:ncardinality is 1:n
19XAO:0004290cell partoio:hasDbXrefGO:0044464obsolete cell partsemapv:UnspecifiedMatchingXAOGO1:1object is obsolete
20XAO:0004615basal bodyoio:hasDbXrefGO:0005932NaNsemapv:UnspecifiedMatchingXAOGO1:1object is obsolete
21XAO:0004621epidermal celloio:hasDbXrefCL:1000396NaNsemapv:UnspecifiedMatchingXAOCL1:1object is obsolete
22XAO:0005007Muller celloio:hasDbXrefCL:0011107obsolete Muller cellsemapv:UnspecifiedMatchingXAOCL1:1object is obsolete
23XAO:1000007tailbud stageoio:hasDbXrefUBERON:0009741obsolete tailbud stagesemapv:UnspecifiedMatchingXAOUBERON1:1object is obsolete
\n", + "
" + ], + "text/plain": [ + " subject_id subject_label predicate_id object_id \\\n", + "0 XAO:0000054 trunk region oio:hasDbXref UBERON:0002100 \n", + "1 XAO:0000100 cardiovascular system oio:hasDbXref UBERON:0004535 \n", + "2 XAO:0000204 peripheral nerve oio:hasDbXref UBERON:0002003 \n", + "3 XAO:0000227 eye primordium oio:hasDbXref UBERON:0003071 \n", + "4 XAO:0000282 visceral pouch oio:hasDbXref UBERON:0004117 \n", + "5 XAO:0000376 omphalomesenteric vein oio:hasDbXref UBERON:0005487 \n", + "6 XAO:0000427 gasserian ganglion oio:hasDbXref UBERON:0001675 \n", + "7 XAO:0000428 trigeminal ganglion oio:hasDbXref UBERON:0001675 \n", + "8 XAO:0001010 circulatory system oio:hasDbXref UBERON:0004535 \n", + "9 XAO:0003001 anatomical group oio:hasDbXref CARO:0000054 \n", + "10 XAO:0003012 cell oio:hasDbXref GO:0005623 \n", + "11 XAO:0003025 trunk oio:hasDbXref UBERON:0002100 \n", + "12 XAO:0003160 anatomical cluster oio:hasDbXref CARO:0000041 \n", + "13 XAO:0003163 basal lamina oio:hasDbXref CARO:0000065 \n", + "14 XAO:0003257 myelin accumulating cell oio:hasDbXref CL:0000328 \n", + "15 XAO:0004090 optic field oio:hasDbXref UBERON:0003071 \n", + "16 XAO:0004147 vitelline vein oio:hasDbXref UBERON:0005487 \n", + "17 XAO:0004165 intersomitic artery oio:hasDbXref UBERON:0006001 \n", + "18 XAO:0004260 pharyngeal pouch oio:hasDbXref UBERON:0004117 \n", + "19 XAO:0004290 cell part oio:hasDbXref GO:0044464 \n", + "20 XAO:0004615 basal body oio:hasDbXref GO:0005932 \n", + "21 XAO:0004621 epidermal cell oio:hasDbXref CL:1000396 \n", + "22 XAO:0005007 Muller cell oio:hasDbXref CL:0011107 \n", + "23 XAO:1000007 tailbud stage oio:hasDbXref UBERON:0009741 \n", + "\n", + " object_label mapping_justification \\\n", + "0 trunk semapv:UnspecifiedMatching \n", + "1 cardiovascular system semapv:UnspecifiedMatching \n", + "2 obsolete peripheral nerve semapv:UnspecifiedMatching \n", + "3 eye primordium semapv:UnspecifiedMatching \n", + "4 pharyngeal pouch semapv:UnspecifiedMatching \n", + "5 vitelline vein semapv:UnspecifiedMatching \n", + "6 trigeminal ganglion semapv:UnspecifiedMatching \n", + "7 trigeminal ganglion semapv:UnspecifiedMatching \n", + "8 cardiovascular system semapv:UnspecifiedMatching \n", + "9 anatomical group semapv:UnspecifiedMatching \n", + "10 obsolete cell semapv:UnspecifiedMatching \n", + "11 trunk semapv:UnspecifiedMatching \n", + "12 anatomical cluster semapv:UnspecifiedMatching \n", + "13 basal lamina semapv:UnspecifiedMatching \n", + "14 obsolete myelin accumulating cell semapv:UnspecifiedMatching \n", + "15 eye primordium semapv:UnspecifiedMatching \n", + "16 vitelline vein semapv:UnspecifiedMatching \n", + "17 NaN semapv:UnspecifiedMatching \n", + "18 pharyngeal pouch semapv:UnspecifiedMatching \n", + "19 obsolete cell part semapv:UnspecifiedMatching \n", + "20 NaN semapv:UnspecifiedMatching \n", + "21 NaN semapv:UnspecifiedMatching \n", + "22 obsolete Muller cell semapv:UnspecifiedMatching \n", + "23 obsolete tailbud stage semapv:UnspecifiedMatching \n", + "\n", + " subject_source object_source mapping_cardinality comment \n", + "0 XAO UBERON 1:n cardinality is 1:n \n", + "1 XAO UBERON 1:n cardinality is 1:n \n", + "2 XAO UBERON 1:1 object is obsolete \n", + "3 XAO UBERON 1:n cardinality is 1:n \n", + "4 XAO UBERON 1:n cardinality is 1:n \n", + "5 XAO UBERON 1:n cardinality is 1:n \n", + "6 XAO UBERON 1:n cardinality is 1:n \n", + "7 XAO UBERON 1:n cardinality is 1:n \n", + "8 XAO UBERON 1:n cardinality is 1:n \n", + "9 XAO CARO 1:1 object is obsolete \n", + "10 XAO GO 1:1 object is obsolete \n", + "11 XAO UBERON 1:n cardinality is 1:n \n", + "12 XAO CARO 1:1 object is obsolete \n", + "13 XAO CARO 1:1 object is obsolete \n", + "14 XAO CL 1:1 object is obsolete \n", + "15 XAO UBERON 1:n cardinality is 1:n \n", + "16 XAO UBERON 1:n cardinality is 1:n \n", + "17 XAO UBERON 1:1 object is obsolete \n", + "18 XAO UBERON 1:n cardinality is 1:n \n", + "19 XAO GO 1:1 object is obsolete \n", + "20 XAO GO 1:1 object is obsolete \n", + "21 XAO CL 1:1 object is obsolete \n", + "22 XAO CL 1:1 object is obsolete \n", + "23 XAO UBERON 1:1 object is obsolete " + ] + }, + "execution_count": 5, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "import pandas as pd\n", + "df = pd.read_csv(\"output/xao-invalid.sssom.tsv\", sep=\"\\t\", comment=\"#\")\n", + "df" + ] + }, + { + "cell_type": "markdown", + "id": "f4209133-fd5c-4ecd-a0c4-a5dc4cb8a57a", + "metadata": {}, + "source": [ + "Here we can see a mixture of cardinality issues and obsoletion issues\n", + "\n", + "Note that behind the scenes this command connected to external ontologies such as GO, CL, and UBERON\n", + "in order to check obsoletion status etc." + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "id": "421c556c-df3e-4281-914b-613e3d467036", + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "array(['cardinality is 1:n', 'object is obsolete'], dtype=object)" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df[\"comment\"].unique()" + ] + }, + { + "cell_type": "code", + "execution_count": 11, + "id": "aea2cfe0-70bf-4b76-89e2-2bfdbdd3a084", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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commentcounts
0cardinality is 1:n12
1object is obsolete12
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" + ], + "text/plain": [ + " comment counts\n", + "0 cardinality is 1:n 12\n", + "1 object is obsolete 12" + ] + }, + "execution_count": 11, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.groupby(\"comment\").size().reset_index(name='counts')" + ] + }, + { + "cell_type": "markdown", + "id": "47d16aab-beae-4797-b2e4-e567db7dd06f", + "metadata": {}, + "source": [ + "## Example: CL\n", + "\n", + "CL has a broader range of mappings, in the ontology as xrefs" + ] + }, + { + "cell_type": "code", + "execution_count": 14, + "id": "59d83f58-058d-43d0-a5f9-17dde3b2af1a", + "metadata": {}, + "outputs": [], + "source": [ + "!runoak --quiet -i sqlite:obo:cl validate-mappings -O sssom -o output/cl-invalid.sssom.tsv >& output/LOG" + ] + }, + { + "cell_type": "code", + "execution_count": 15, + "id": "2515b428-1d54-4756-a429-9ca21002e0d4", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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subject_idsubject_labelpredicate_idobject_idobject_labelmapping_justificationsubject_sourceobject_sourcemapping_cardinalitycomment
0CARO:0000013celloio:hasDbXrefGO:0005623obsolete cellsemapv:UnspecifiedMatchingCAROGO1:1object is obsolete
1CL:0000000celloio:hasDbXrefGO:0005623obsolete cellsemapv:UnspecifiedMatchingCLGO1:1object is obsolete
2CL:0000019spermoio:hasDbXrefBTO:0001277spermatozoonsemapv:UnspecifiedMatchingCLBTOn:ncardinality is n:n
3CL:0000019spermoio:hasDbXrefBTO:0002046spermatozoidsemapv:UnspecifiedMatchingCLBTOn:1cardinality is n:1
4CL:0000019spermoio:hasDbXrefCALOHA:TS-0949NaNsemapv:UnspecifiedMatchingCLCALOHA1:ncardinality is 1:n
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3824UBERON:2001316anterior lateral line placodeoio:hasDbXrefEFO:0003461obsolete_anterior lateral line placodesemapv:UnspecifiedMatchingUBERONEFO1:1object is obsolete
3825UBERON:2001389regeneration epithelium of fin/limboio:hasDbXrefEFO:0003682obsolete_regeneration epitheliumsemapv:UnspecifiedMatchingUBERONEFO1:1object is obsolete
3826UBERON:2001391anterior lateral line ganglionoio:hasDbXrefEFO:0003683obsolete_anterior lateral line ganglionsemapv:UnspecifiedMatchingUBERONEFO1:1object is obsolete
3827UBERON:2001468anterior lateral line systemoio:hasDbXrefEFO:0003691obsolete_anterior lateral line systemsemapv:UnspecifiedMatchingUBERONEFO1:1object is obsolete
3828UBERON:6000004panarthropod headoio:hasDbXrefFBbt:00000004headsemapv:UnspecifiedMatchingUBERONFBbt1:ncardinality is 1:n
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3829 rows × 10 columns

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" + ], + "text/plain": [ + " subject_id subject_label predicate_id \\\n", + "0 CARO:0000013 cell oio:hasDbXref \n", + "1 CL:0000000 cell oio:hasDbXref \n", + "2 CL:0000019 sperm oio:hasDbXref \n", + "3 CL:0000019 sperm oio:hasDbXref \n", + "4 CL:0000019 sperm oio:hasDbXref \n", + "... ... ... ... \n", + "3824 UBERON:2001316 anterior lateral line placode oio:hasDbXref \n", + "3825 UBERON:2001389 regeneration epithelium of fin/limb oio:hasDbXref \n", + "3826 UBERON:2001391 anterior lateral line ganglion oio:hasDbXref \n", + "3827 UBERON:2001468 anterior lateral line system oio:hasDbXref \n", + "3828 UBERON:6000004 panarthropod head oio:hasDbXref \n", + "\n", + " object_id object_label \\\n", + "0 GO:0005623 obsolete cell \n", + "1 GO:0005623 obsolete cell \n", + "2 BTO:0001277 spermatozoon \n", + "3 BTO:0002046 spermatozoid \n", + "4 CALOHA:TS-0949 NaN \n", + "... ... ... \n", + "3824 EFO:0003461 obsolete_anterior lateral line placode \n", + "3825 EFO:0003682 obsolete_regeneration epithelium \n", + "3826 EFO:0003683 obsolete_anterior lateral line ganglion \n", + "3827 EFO:0003691 obsolete_anterior lateral line system \n", + "3828 FBbt:00000004 head \n", + "\n", + " mapping_justification subject_source object_source \\\n", + "0 semapv:UnspecifiedMatching CARO GO \n", + "1 semapv:UnspecifiedMatching CL GO \n", + "2 semapv:UnspecifiedMatching CL BTO \n", + "3 semapv:UnspecifiedMatching CL BTO \n", + "4 semapv:UnspecifiedMatching CL CALOHA \n", + "... ... ... ... \n", + "3824 semapv:UnspecifiedMatching UBERON EFO \n", + "3825 semapv:UnspecifiedMatching UBERON EFO \n", + "3826 semapv:UnspecifiedMatching UBERON EFO \n", + "3827 semapv:UnspecifiedMatching UBERON EFO \n", + "3828 semapv:UnspecifiedMatching UBERON FBbt \n", + "\n", + " mapping_cardinality comment \n", + "0 1:1 object is obsolete \n", + "1 1:1 object is obsolete \n", + "2 n:n cardinality is n:n \n", + "3 n:1 cardinality is n:1 \n", + "4 1:n cardinality is 1:n \n", + "... ... ... \n", + "3824 1:1 object is obsolete \n", + "3825 1:1 object is obsolete \n", + "3826 1:1 object is obsolete \n", + "3827 1:1 object is obsolete \n", + "3828 1:n cardinality is 1:n \n", + "\n", + "[3829 rows x 10 columns]" + ] + }, + "execution_count": 15, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df = pd.read_csv(\"output/cl-invalid.sssom.tsv\", sep=\"\\t\", comment=\"#\")\n", + "df" + ] + }, + { + "cell_type": "code", + "execution_count": 16, + "id": "0723f096-67d4-4727-bf77-13badec03878", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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commentcounts
0cardinality is 1:n608
1cardinality is n:12588
2cardinality is n:n155
3object is obsolete438
4object is obsolete | cardinality is n:19
5subject is obsolete13
6subject is obsolete | cardinality is 1:n11
7subject is obsolete | object is obsolete2
\n", + "
" + ], + "text/plain": [ + " comment counts\n", + "0 cardinality is 1:n 608\n", + "1 cardinality is n:1 2588\n", + "2 cardinality is n:n 155\n", + "3 object is obsolete 438\n", + "4 object is obsolete | cardinality is n:1 9\n", + "5 subject is obsolete 13\n", + "6 subject is obsolete | cardinality is 1:n 11\n", + "7 subject is obsolete | object is obsolete 2" + ] + }, + "execution_count": 16, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.groupby(\"comment\").size().reset_index(name='counts')" + ] + }, + { + "cell_type": "markdown", + "id": "69020950-4636-4ec3-a03b-a552a837f3f9", + "metadata": {}, + "source": [ + "We can summarize these in groups:" + ] + }, + { + "cell_type": "code", + "execution_count": 18, + "id": "8af2fb74-91ec-4c61-90a9-68c860a6e16a", + "metadata": {}, + "outputs": [ + { + "data": { + "text/html": [ + "
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commentsubject_sourceobject_sourcecounts
0cardinality is 1:nCLBTO35
1cardinality is 1:nCLCALOHA25
2cardinality is 1:nCLFAO3
3cardinality is 1:nCLFMA20
4cardinality is 1:nCLGOC4
...............
121subject is obsolete | cardinality is 1:nCLFAO1
122subject is obsolete | cardinality is 1:nCLFMA3
123subject is obsolete | cardinality is 1:nCLILX6
124subject is obsolete | object is obsoleteCLFBbt1
125subject is obsolete | object is obsoleteRORO1
\n", + "

126 rows × 4 columns

\n", + "
" + ], + "text/plain": [ + " comment subject_source object_source \\\n", + "0 cardinality is 1:n CL BTO \n", + "1 cardinality is 1:n CL CALOHA \n", + "2 cardinality is 1:n CL FAO \n", + "3 cardinality is 1:n CL FMA \n", + "4 cardinality is 1:n CL GOC \n", + ".. ... ... ... \n", + "121 subject is obsolete | cardinality is 1:n CL FAO \n", + "122 subject is obsolete | cardinality is 1:n CL FMA \n", + "123 subject is obsolete | cardinality is 1:n CL ILX \n", + "124 subject is obsolete | object is obsolete CL FBbt \n", + "125 subject is obsolete | object is obsolete RO RO \n", + "\n", + " counts \n", + "0 35 \n", + "1 25 \n", + "2 3 \n", + "3 20 \n", + "4 4 \n", + ".. ... \n", + "121 1 \n", + "122 3 \n", + "123 6 \n", + "124 1 \n", + "125 1 \n", + "\n", + "[126 rows x 4 columns]" + ] + }, + "execution_count": 18, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "df.groupby([\"comment\", \"subject_source\", \"object_source\"]).size().reset_index(name='counts')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "d699f471-d70a-4f3e-aac4-3cdd55e66380", + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3 (ipykernel)", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.9.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/poetry.lock b/poetry.lock index 94390c871..b11b817ff 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,9 +1,10 @@ -# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. [[package]] name = "adeft" version = "0.11.2" description = "Acromine based Disambiguation of Entities From Text" +category = "main" optional = true python-versions = "*" files = [ @@ -24,6 +25,7 @@ test = ["pytest", "pytest-cov"] name = "airium" version = "0.2.5" description = "Easy and quick html builder with natural syntax correspondence (python->html). No templates needed. Serves pure pythonic library with no dependencies." +category = "main" optional = false python-versions = "*" files = [ @@ -39,6 +41,7 @@ parse = ["beautifulsoup4 (>=4.10,<5.0)", "requests (>=2.12,<3)"] name = "alabaster" version = "0.7.13" description = "A configurable sidebar-enabled Sphinx theme" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -50,6 +53,7 @@ files = [ name = "aniso8601" version = "9.0.1" description = "A library for parsing ISO 8601 strings." +category = "main" optional = true python-versions = "*" files = [ @@ -64,6 +68,7 @@ dev = ["black", "coverage", "isort", "pre-commit", "pyenchant", "pylint"] name = "annotated-types" version = "0.5.0" description = "Reusable constraint types to use with typing.Annotated" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -75,6 +80,7 @@ files = [ name = "antlr4-python3-runtime" version = "4.9.3" description = "ANTLR 4.9.3 runtime for Python 3.7" +category = "main" optional = false python-versions = "*" files = [ @@ -85,6 +91,7 @@ files = [ name = "anyio" version = "3.7.1" description = "High level compatibility layer for multiple asynchronous event loop implementations" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -106,6 +113,7 @@ trio = ["trio (<0.22)"] name = "appdirs" version = "1.4.4" description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"." +category = "main" optional = false python-versions = "*" files = [ @@ -117,6 +125,7 @@ files = [ name = "appnope" version = "0.1.3" description = "Disable App Nap on macOS >= 10.9" +category = "dev" optional = false python-versions = "*" files = [ @@ -126,27 +135,30 @@ files = [ [[package]] name = "argon2-cffi" -version = "21.3.0" -description = "The secure Argon2 password hashing algorithm." +version = "23.1.0" +description = "Argon2 for Python" +category = "dev" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" files = [ - {file = "argon2-cffi-21.3.0.tar.gz", hash = "sha256:d384164d944190a7dd7ef22c6aa3ff197da12962bd04b17f64d4e93d934dba5b"}, - {file = "argon2_cffi-21.3.0-py3-none-any.whl", hash = "sha256:8c976986f2c5c0e5000919e6de187906cfd81fb1c72bf9d88c01177e77da7f80"}, + {file = "argon2_cffi-23.1.0-py3-none-any.whl", hash = "sha256:c670642b78ba29641818ab2e68bd4e6a78ba53b7eff7b4c3815ae16abf91c7ea"}, + {file = "argon2_cffi-23.1.0.tar.gz", hash = "sha256:879c3e79a2729ce768ebb7d36d4609e3a78a4ca2ec3a9f12286ca057e3d0db08"}, ] [package.dependencies] argon2-cffi-bindings = "*" [package.extras] -dev = ["cogapp", "coverage[toml] (>=5.0.2)", "furo", "hypothesis", "pre-commit", "pytest", "sphinx", "sphinx-notfound-page", "tomli"] -docs = ["furo", "sphinx", "sphinx-notfound-page"] -tests = ["coverage[toml] (>=5.0.2)", "hypothesis", "pytest"] +dev = ["argon2-cffi[tests,typing]", "tox (>4)"] +docs = ["furo", "myst-parser", "sphinx", "sphinx-copybutton", "sphinx-notfound-page"] +tests = ["hypothesis", "pytest"] +typing = ["mypy"] [[package]] name = "argon2-cffi-bindings" version = "21.2.0" description = "Low-level CFFI bindings for Argon2" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -184,6 +196,7 @@ tests = ["pytest"] name = "arrow" version = "1.2.3" description = "Better dates & times for Python" +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -198,6 +211,7 @@ python-dateutil = ">=2.7.0" name = "asttokens" version = "2.2.1" description = "Annotate AST trees with source code positions" +category = "dev" optional = false python-versions = "*" files = [ @@ -215,6 +229,7 @@ test = ["astroid", "pytest"] name = "async-lru" version = "2.0.4" description = "Simple LRU cache for asyncio" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -229,6 +244,7 @@ typing-extensions = {version = ">=4.0.0", markers = "python_version < \"3.11\""} name = "attrs" version = "23.1.0" description = "Classes Without Boilerplate" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -247,6 +263,7 @@ tests-no-zope = ["cloudpickle", "hypothesis", "mypy (>=1.1.1)", "pympler", "pyte name = "babel" version = "2.12.1" description = "Internationalization utilities" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -258,6 +275,7 @@ files = [ name = "backcall" version = "0.2.0" description = "Specifications for callback functions passed in to an API" +category = "dev" optional = false python-versions = "*" files = [ @@ -269,6 +287,7 @@ files = [ name = "bcp47" version = "0.0.4" description = "Language tags made easy" +category = "main" optional = false python-versions = "*" files = [ @@ -280,6 +299,7 @@ files = [ name = "beautifulsoup4" version = "4.12.2" description = "Screen-scraping library" +category = "main" optional = false python-versions = ">=3.6.0" files = [ @@ -298,6 +318,7 @@ lxml = ["lxml"] name = "bleach" version = "6.0.0" description = "An easy safelist-based HTML-sanitizing tool." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -314,17 +335,18 @@ css = ["tinycss2 (>=1.1.0,<1.2)"] [[package]] name = "boto3" -version = "1.28.21" +version = "1.28.34" description = "The AWS SDK for Python" +category = "main" optional = true python-versions = ">= 3.7" files = [ - {file = "boto3-1.28.21-py3-none-any.whl", hash = "sha256:28e1ea098e43e764d990b4466e377c322b5d57829e2eb1395eca52d4209a6c11"}, - {file = "boto3-1.28.21.tar.gz", hash = "sha256:0ad6932b2469f4fa4e63f4baf8508ccc1b1bc215b9c835df73505aa85210fc27"}, + {file = "boto3-1.28.34-py3-none-any.whl", hash = "sha256:2ccbea42fe4cbd22a8ba1e90a37ac65f05c1932e63432e429fb7158d8255bbc0"}, + {file = "boto3-1.28.34.tar.gz", hash = "sha256:4713a4e69120db5f358f4d378459fb4ea04be98664a0908088f6e04ab49d2583"}, ] [package.dependencies] -botocore = ">=1.31.21,<1.32.0" +botocore = ">=1.31.34,<1.32.0" jmespath = ">=0.7.1,<2.0.0" s3transfer = ">=0.6.0,<0.7.0" @@ -333,13 +355,14 @@ crt = ["botocore[crt] (>=1.21.0,<2.0a0)"] [[package]] name = "botocore" -version = "1.31.21" +version = "1.31.34" description = "Low-level, data-driven core of boto 3." +category = "main" optional = true python-versions = ">= 3.7" files = [ - {file = "botocore-1.31.21-py3-none-any.whl", hash = "sha256:c20a5c46eaf49b18b76fdfaec5583320e18abd551b1bc3cd7b1e718372675e21"}, - {file = "botocore-1.31.21.tar.gz", hash = "sha256:9a13736b16aea3f16829b00edfb2c656fee72ecbfe5eb396cc2f8632e31fd524"}, + {file = "botocore-1.31.34-py3-none-any.whl", hash = "sha256:23ba9e3a8b4c0e5966bbe2db62edb27f61e16b846f153f22aefda7b3c05c7942"}, + {file = "botocore-1.31.34.tar.gz", hash = "sha256:456ef8eb458db35b8643eb10e652ed50750d13e5af431593471b2c705c34b5db"}, ] [package.dependencies] @@ -354,6 +377,7 @@ crt = ["awscrt (==0.16.26)"] name = "cattrs" version = "23.1.2" description = "Composable complex class support for attrs and dataclasses." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -379,6 +403,7 @@ ujson = ["ujson (>=5.4.0,<6.0.0)"] name = "certifi" version = "2023.7.22" description = "Python package for providing Mozilla's CA Bundle." +category = "main" optional = false python-versions = ">=3.6" files = [ @@ -390,6 +415,7 @@ files = [ name = "cffi" version = "1.15.1" description = "Foreign Function Interface for Python calling C code." +category = "dev" optional = false python-versions = "*" files = [ @@ -466,6 +492,7 @@ pycparser = "*" name = "cfgraph" version = "0.2.1" description = "rdflib collections flattening graph" +category = "dev" optional = false python-versions = "*" files = [ @@ -479,6 +506,7 @@ rdflib = ">=0.4.2" name = "chardet" version = "5.2.0" description = "Universal encoding detector for Python 3" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -490,6 +518,7 @@ files = [ name = "charset-normalizer" version = "3.2.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." +category = "main" optional = false python-versions = ">=3.7.0" files = [ @@ -574,6 +603,7 @@ files = [ name = "class-resolver" version = "0.4.2" description = "Lookup and instantiate classes with style." +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -598,13 +628,14 @@ torch-geometric = ["torch", "torch-geometric", "torch-sparse"] [[package]] name = "click" -version = "8.1.6" +version = "8.1.7" description = "Composable command line interface toolkit" +category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "click-8.1.6-py3-none-any.whl", hash = "sha256:fa244bb30b3b5ee2cae3da8f55c9e5e0c0e86093306301fb418eb9dc40fbded5"}, - {file = "click-8.1.6.tar.gz", hash = "sha256:48ee849951919527a045bfe3bf7baa8a959c423134e1a5b98c05c20ba75a1cbd"}, + {file = "click-8.1.7-py3-none-any.whl", hash = "sha256:ae74fb96c20a0277a1d615f1e4d73c8414f5a98db8b799a7931d1582f3390c28"}, + {file = "click-8.1.7.tar.gz", hash = "sha256:ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de"}, ] [package.dependencies] @@ -614,6 +645,7 @@ colorama = {version = "*", markers = "platform_system == \"Windows\""} name = "colorama" version = "0.4.6" description = "Cross-platform colored terminal text." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7" files = [ @@ -625,6 +657,7 @@ files = [ name = "comm" version = "0.1.4" description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc." +category = "dev" optional = false python-versions = ">=3.6" files = [ @@ -644,6 +677,7 @@ typing = ["mypy (>=0.990)"] name = "contourpy" version = "1.1.0" description = "Python library for calculating contours of 2D quadrilateral grids" +category = "dev" optional = false python-versions = ">=3.8" files = [ @@ -702,6 +736,7 @@ test-no-images = ["pytest", "pytest-cov", "wurlitzer"] name = "coverage" 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+5735,7 @@ test = ["argcomplete (>=2.0)", "pre-commit", "pytest", "pytest-mock"] name = "typing-extensions" version = "4.7.1" description = "Backported and Experimental Type Hints for Python 3.7+" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5363,6 +5747,7 @@ files = [ name = "tzdata" version = "2023.3" description = "Provider of IANA time zone data" +category = "main" optional = false python-versions = ">=2" files = [ @@ -5374,6 +5759,7 @@ files = [ name = "unidecode" version = "1.3.6" description = "ASCII transliterations of Unicode text" +category = "main" optional = true python-versions = ">=3.5" files = [ @@ -5385,6 +5771,7 @@ files = [ name = "uri-template" version = "1.3.0" description = "RFC 6570 URI Template Processor" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -5399,6 +5786,7 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake name = "url-normalize" version = "1.4.3" description = 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= [ @@ -5455,6 +5851,7 @@ files = [ name = "watchdog" version = "3.0.0" description = "Filesystem events monitoring" +category = "main" optional = false python-versions = ">=3.7" files = [ @@ -5494,6 +5891,7 @@ watchmedo = ["PyYAML (>=3.10)"] name = "wcwidth" version = "0.2.6" description = "Measures the displayed width of unicode strings in a terminal" +category = "dev" optional = false python-versions = "*" files = [ @@ -5505,6 +5903,7 @@ files = [ name = "webcolors" version = "1.13" description = "A library for working with the color formats defined by HTML and CSS." +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -5520,6 +5919,7 @@ tests = ["pytest", "pytest-cov"] name = "webencodings" version = "0.5.1" description = "Character encoding aliases for legacy web content" +category = "dev" optional = false python-versions = "*" files = [ @@ -5529,17 +5929,18 @@ files = [ [[package]] name = "websocket-client" -version = "1.6.1" +version = "1.6.2" description = 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application library." +category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5561,6 +5963,7 @@ watchdog = ["watchdog"] name = "widgetsnbextension" version = "4.0.8" description = "Jupyter interactive widgets for Jupyter Notebook" +category = "dev" optional = false python-versions = ">=3.7" files = [ @@ -5572,6 +5975,7 @@ files = [ name = "wrapt" version = "1.15.0" description = "Module for decorators, wrappers and monkey patching." +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" files = [ @@ -5656,6 +6060,7 @@ files = [ name = "wtforms" version = "3.0.1" description = "Form validation and rendering for Python web development." +category = "main" optional = true python-versions = ">=3.7" files = [ @@ -5673,6 +6078,7 @@ email = ["email-validator"] name = "zipp" version = "3.16.2" description = "Backport of pathlib-compatible object wrapper for zip files" +category = "main" optional = false python-versions = ">=3.8" files = [ diff --git a/src/oaklib/cli.py b/src/oaklib/cli.py index 001461ae7..53639a144 100644 --- a/src/oaklib/cli.py +++ b/src/oaklib/cli.py @@ -4943,6 +4943,61 @@ def validate_definitions(terms, skip_text_annotation, output: str, output_type: raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") +@main.command() +@autolabel_option +@output_type_option +@click.option( + "--adapter-mapping", + multiple=True, + help="Multiple prefix=selector pairs, e.g. --adapter-mapping uberon=db/uberon.db", +) +@output_option +@click.argument("terms", nargs=-1) +def validate_mappings(terms, autolabel, adapter_mapping, output: str, output_type: str): + """ + Validates mappings in ontology using additional ontologies. + + To run: + + runoak validate-mappings -i db/uberon.db + + For sssom: + + runoak validate-mappings -i db/uberon.db -o bad-mappings.sssom.tsv + + By default this will attempt to download and connect to + sqlite versions of different ontologies. + + You can customize this: + + runoak validate-mappings -i db/uberon.db --adapter-mapping uberon=db/uberon.db \ + --adapter-mapping zfa=db/zfa.db + + You can use "*" as a wildcard, in the case where you have an application ontology + with many mapped entities merged in: + + runoak validate-mappings -i db/uberon.db --adapter-mapping "*"=db/merged.db" + """ + impl = settings.impl + writer = _get_writer(output_type, impl, StreamingYamlWriter, datamodel=sssom_schema) + writer.output = output + writer.autolabel = autolabel + if not isinstance(impl, MappingProviderInterface): + raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") + mappings = list(impl.sssom_mappings()) + logging.info(f"Loaded {len(mappings)} mappings") + import oaklib.utilities.mapping.mapping_validation as mapping_validation + + adapters = {} + for am in adapter_mapping: + prefix, selector = am.split("=") + adapters[prefix] = get_adapter(selector) + logging.info(f"Loaded adapter for {prefix} => {selector}") + for _, mapping in mapping_validation.validate_mappings(mappings, adapters=adapters): + writer.emit(mapping) + writer.finish() + + @main.command() @click.argument("curie_pairs", nargs=-1) @click.option( @@ -5137,49 +5192,48 @@ def lexmatch( # if exclude_tokens: # token_exclusion_list = get_exclusion_token_list(exclude_tokens) - if isinstance(impl, BasicOntologyInterface): - if terms: - if "@" in terms: - ix = terms.index("@") - logging.info(f"Splitting terms into two, position = {ix}") - subjects = list(query_terms_iterator(terms[0:ix], impl)) - objects = list(query_terms_iterator(terms[ix + 1 :], impl)) - else: - subjects = list(query_terms_iterator(terms, impl)) - objects = subjects - else: - subjects = None - objects = None - if add_labels: - add_labels_from_uris(impl) - if not recreate and Path(lexical_index_file).exists(): - logging.info("Reusing previous index") - ix = load_lexical_index(lexical_index_file) + if not isinstance(impl, BasicOntologyInterface): + raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") + if terms: + if "@" in terms: + ix = terms.index("@") + logging.info(f"Splitting terms into two, position = {ix}") + subjects = list(query_terms_iterator(terms[0:ix], impl)) + objects = list(query_terms_iterator(terms[ix + 1 :], impl)) else: - logging.info("Creating index") - if ruleset: - syn_rules = [x.synonymizer for x in ruleset.rules if x.synonymizer] - else: - syn_rules = [] - ix = create_lexical_index(impl, synonym_rules=syn_rules) - if lexical_index_file: - if recreate: - logging.info("Saving index") - save_lexical_index(ix, lexical_index_file) - logging.info(f"Generating mappings from {len(ix.groupings)} groupings") - # TODO: abstract this way from serialization format - msdf = lexical_index_to_sssom( - impl, - ix, - ruleset=ruleset, - subjects=subjects, - objects=objects, - prefix_map=prefix_map, - ensure_strict_prefixes=ensure_strict_prefixes, - ) - sssom_writers.write_table(msdf, output) + subjects = list(query_terms_iterator(terms, impl)) + objects = subjects else: - raise NotImplementedError(f"Cannot execute this using {impl} of type {type(impl)}") + subjects = None + objects = None + if add_labels: + add_labels_from_uris(impl) + if not recreate and Path(lexical_index_file).exists(): + logging.info("Reusing previous index") + ix = load_lexical_index(lexical_index_file) + else: + logging.info("Creating index") + if ruleset: + syn_rules = [x.synonymizer for x in ruleset.rules if x.synonymizer] + else: + syn_rules = [] + ix = create_lexical_index(impl, synonym_rules=syn_rules) + if lexical_index_file: + if recreate: + logging.info("Saving index") + save_lexical_index(ix, lexical_index_file) + logging.info(f"Generating mappings from {len(ix.groupings)} groupings") + # TODO: abstract this way from serialization format + msdf = lexical_index_to_sssom( + impl, + ix, + ruleset=ruleset, + subjects=subjects, + objects=objects, + prefix_map=prefix_map, + ensure_strict_prefixes=ensure_strict_prefixes, + ) + sssom_writers.write_table(msdf, output) @main.command() diff --git a/src/oaklib/implementations/kgx/kgx_implementation.py b/src/oaklib/implementations/kgx/kgx_implementation.py index 9b650e594..77049c5f4 100644 --- a/src/oaklib/implementations/kgx/kgx_implementation.py +++ b/src/oaklib/implementations/kgx/kgx_implementation.py @@ -367,7 +367,9 @@ def label(self, curie: CURIE, **kwargs) -> Optional[str]: for row in q: return row[0] - def labels(self, curies: Iterable[CURIE], allow_none=True) -> Iterable[Tuple[CURIE, str]]: + def labels( + self, curies: Iterable[CURIE], allow_none=True, **kwargs + ) -> Iterable[Tuple[CURIE, str]]: for curie_it in chunk(curies, self.max_items_for_in_clause): curr_curies = list(curie_it) has_label = set() diff --git a/src/oaklib/implementations/sqldb/sql_implementation.py b/src/oaklib/implementations/sqldb/sql_implementation.py index d6e10ae36..53f8f62d7 100644 --- a/src/oaklib/implementations/sqldb/sql_implementation.py +++ b/src/oaklib/implementations/sqldb/sql_implementation.py @@ -2590,11 +2590,14 @@ def _filter(select_expr, filter_expr=None): if branch_subq: match_query = match_query.filter(Statements.subject.in_(branch_subq)) subject_ids_by_object_source = defaultdict(list) + bad_ids = set() for row in match_query: subject_id = row.subject object_id = row.value if row.value else row.object if ":" not in object_id: - logging.warning(f"bad mapping: {object_id}") + if object_id not in bad_ids: + logging.warning(f"bad mapping: {object_id}") + bad_ids.add(object_id) object_source = object_id.split(":")[0] subject_ids_by_object_source[object_source].append(subject_id) for object_source, subject_ids in subject_ids_by_object_source.items(): diff --git a/src/oaklib/utilities/mapping/mapping_validation.py b/src/oaklib/utilities/mapping/mapping_validation.py index 882cbf5a3..9904340c4 100644 --- a/src/oaklib/utilities/mapping/mapping_validation.py +++ b/src/oaklib/utilities/mapping/mapping_validation.py @@ -1,8 +1,14 @@ -from typing import Iterator +import logging +from collections import defaultdict +from copy import deepcopy +from typing import Dict, Iterator, List, Optional, Tuple -from sssom_schema import Mapping +from sssom_schema import Mapping, MappingCardinalityEnum -from oaklib.interfaces import MappingProviderInterface +from oaklib import get_adapter +from oaklib.datamodels.vocabulary import HAS_DBXREF, SKOS_EXACT_MATCH +from oaklib.interfaces import BasicOntologyInterface, MappingProviderInterface +from oaklib.types import CURIE from oaklib.utilities.mapping.cross_ontology_diffs import ( group_mappings_by_source_pairs, object_source, @@ -10,6 +16,10 @@ ) +def _prefix(curie: CURIE) -> str: + return curie.split(":")[0].lower() + + def unreciprocated_mappings( subject_oi: MappingProviderInterface, object_oi: MappingProviderInterface, @@ -59,3 +69,172 @@ def unreciprocated_mappings( both_directions=False, ): yield m + + +def partition_mappings( + mappings: List[Mapping], +) -> Dict[Tuple[str, str], List[Mapping]]: + """ + Partition mappings by subject and object prefixes. + + >>> from oaklib import get_adapter + >>> from oaklib.utilities.mapping.mapping_validation import partition_mappings + >>> adapter = get_adapter("sqlite:obo:xao") + >>> mappings = list(adapter.sssom_mappings()) + >>> by_prefixes = partition_mappings(mappings) + >>> for prefix_pair, mappings in partition_mappings(mappings).items(): + ... for mapping in mappings: + ... print(prefix_pair, mapping.subject_id, mapping.object_id) + + ... + ('xao', 'cl') XAO:0003252 CL:0000311 + ... + + :param mappings: + :return: + """ + partitioned = defaultdict(list) + for m in mappings: + subject_prefix = _prefix(m.subject_id) + object_prefix = _prefix(m.object_id) + k = (subject_prefix, object_prefix) + partitioned[k].append(m) + return partitioned + + +def assign_mapping_cardinalities( + mappings: List[Mapping], +) -> None: + groups = partition_mappings(mappings) + for _, mappings in groups.items(): + s2o = defaultdict(set) + o2s = defaultdict(set) + for m in mappings: + s2o[m.subject_id].add(m.object_id) + o2s[m.object_id].add(m.subject_id) + for m in mappings: + + def _card(n: int) -> str: + if n == 1: + return "1" + elif n == 0: + return "0" + else: + return "n" + + card_str = f"{_card(len(s2o[m.subject_id]))}:{_card(len(o2s[m.object_id]))}" + m.mapping_cardinality = MappingCardinalityEnum(MappingCardinalityEnum[card_str]) + + +# TODO: avoid globals +obsoletes = {} + + +def _obsoletes(prefix: str, adapters: Optional[Dict[str, BasicOntologyInterface]]) -> List[CURIE]: + if prefix not in obsoletes: + adapter = _adapter(prefix, adapters) + obsoletes[prefix] = list(adapter.obsoletes(include_merged=True)) + return obsoletes[prefix] + + +def _adapter( + curie: CURIE, adapters: Optional[Dict[str, BasicOntologyInterface]] +) -> Optional[BasicOntologyInterface]: + prefix = _prefix(curie) + if "*" in adapters: + adapters[prefix] = adapters["*"] + if prefix not in obsoletes: + obsoletes[prefix] = list(adapters[prefix].obsoletes(include_merged=True)) + if prefix not in adapters: + logging.info(f"loading {prefix}") + try: + adapters[prefix] = get_adapter(f"sqlite:obo:{prefix}") + except Exception as e: + logging.info(f"failed to load {prefix}: {e}") + adapters[prefix] = None + obsoletes[prefix] = [] + return None + obsoletes[prefix] = list(adapters[prefix].obsoletes(include_merged=True)) + return adapters[prefix] + + +def validate_mappings( + mappings: List[Mapping], + adapters: Optional[Dict[str, BasicOntologyInterface]] = None, + autolabel: bool = True, + xref_is_bijective=True, + inject_comments=True, +) -> Iterator[Tuple[List[str], Mapping]]: + """ + Validate a list of mappings. + + >>> from oaklib import get_adapter + >>> from oaklib.utilities.mapping.mapping_validation import validate_mappings + >>> adapter = get_adapter("sqlite:obo:xao") + >>> mappings = list(adapter.sssom_mappings()) + >>> for errors, m in validate_mappings(mappings): + ... print(errors, m.subject_id, m.object_id) + + ... + + + The current validation checks involve: + + - cardinality checks + - mappings to obsoletes + + For cardinality checks, the assumption is that if the mapping is not 1:1, AND either the predicate + is skos:exactMatch OR oio:hasDbXref, then the mapping is invalid. The oio predicate can be + omitted from this check by setting xref_is_bijective to False. + + Note that for autolabeling and obsoletion checks, it may be necessary to look up + CURIEs in a variety of different ontolgies. The default assumption here is that there + exists a resource ``sqlite:obo:{prefix}`` for each prefix in the CURIEs. This may not always + hold (the xref may not always be to an ontology in the registry), so if no such adapter is found, + the autolabeling and obsoletion checks will be skipped for that CURIE. + + The caller has the option of providing more fine-grained control over the adapters used by + passing an ``adapters`` dict which maps prefixes to ontology adapters. + + The ``adapters`` dict has a special value "*" which will match any prefix -- this can be used in the case + of application ontologies that merge multiple ontologies together. + + :param mappings: mappings to validate + :param adapters: a mapping from prefix to ontology adapter. If not provided, will be created + :param autolabel: if True, will attempt to autolabel the yielded mappings + :param xref_is_bijective: if True (default), then mappings to oio:hasDbXref are considered bijective + :param inject_comments: if True (default), then validation comments will be injected into the mapping + :return: yields all (copy of) mappings that do not validate together with list of problems + """ + if adapters is None: + adapters = {} + + mappings = deepcopy(mappings) + assign_mapping_cardinalities(mappings) + + for m in mappings: + subject_prefix = _prefix(m.subject_id) + object_prefix = _prefix(m.object_id) + if subject_prefix == "_" or object_prefix == "_": + continue + subject_adapter = _adapter(m.subject_id, adapters) + object_adapter = _adapter(m.object_id, adapters) + comments = [] + if m.subject_id in _obsoletes(subject_prefix, adapters): + comments.append("subject is obsolete") + if m.object_id in _obsoletes(object_prefix, adapters): + comments.append("object is obsolete") + if m.mapping_cardinality != MappingCardinalityEnum(MappingCardinalityEnum["1:1"]): + if m.predicate_id == SKOS_EXACT_MATCH or ( + m.predicate_id == HAS_DBXREF and xref_is_bijective + ): + comments.append(f"cardinality is {m.mapping_cardinality}") + if comments: + if autolabel: + if not m.subject_label and subject_adapter: + m.subject_label = subject_adapter.label(m.subject_id) + if not m.object_label and object_adapter: + m.object_label = object_adapter.label(m.object_id) + if inject_comments: + m.comment = " | ".join(comments) + yield comments, m diff --git a/tests/test_utilities/test_mapping_validation.py b/tests/test_utilities/test_mapping_validation.py new file mode 100644 index 000000000..8434a3b56 --- /dev/null +++ b/tests/test_utilities/test_mapping_validation.py @@ -0,0 +1,56 @@ +import unittest + +from sssom_schema import Mapping + +from oaklib import get_adapter +from oaklib.datamodels.vocabulary import IS_A, PART_OF, SEMAPV, SKOS_EXACT_MATCH +from oaklib.utilities.mapping.mapping_validation import validate_mappings +from tests import CYTOPLASM, FUNGI, INPUT_DIR, NUCLEUS, OUTPUT_DIR, VACUOLE + +DB = INPUT_DIR / "go-nucleus.db" +TEST_ONT = INPUT_DIR / "go-nucleus.obo" +TEST_OUT = OUTPUT_DIR / "go-nucleus.saved.owl" + +PREDS = [IS_A, PART_OF] + +# these are biologically nonsensical, the purpose +# is purely to test structural properties +cases = [ + ( + [ + (NUCLEUS, SKOS_EXACT_MATCH, CYTOPLASM), + (NUCLEUS, SKOS_EXACT_MATCH, VACUOLE), + ], + 2, + ), + ( + [ + (NUCLEUS, SKOS_EXACT_MATCH, CYTOPLASM), + (FUNGI, SKOS_EXACT_MATCH, VACUOLE), + ], + 0, + ), +] + + +class TestMappingValidation(unittest.TestCase): + def setUp(self) -> None: + self.adaptor = get_adapter(DB) + self.adapters = { + "go": self.adaptor, + } + + def test_mapping_validation(self): + for case in cases: + tuples, expected_n = case + mappings = [ + Mapping( + subject_id=t[0], + predicate_id=t[1], + object_id=t[2], + mapping_justification=SEMAPV.LexicalMatching.value, + ) + for t in tuples + ] + results = list(validate_mappings(mappings, self.adapters)) + self.assertEqual(case[1], len(results))