diff --git a/.github/workflows/wikidata.yml b/.github/workflows/wikidata.yml index fa2d444f..8508dbbb 100644 --- a/.github/workflows/wikidata.yml +++ b/.github/workflows/wikidata.yml @@ -72,11 +72,11 @@ jobs: echo 'Accessing the Wikidata data' ## Download outdated IDs for chemicals qLever Style - curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/chemicalAllRedirects.rq -G https://qlever.cs.uni-freiburg.de/api/wikidata -o datasources/wikidata/recentData/metabolites.tsv + curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/chemicalAllRedirects.rq -G https://qlever.dev/api/wikidata -o datasources/wikidata/recentData/metabolites.tsv ## Download outdated IDs for genes qLever Style - curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/geneHumanAllRedirects.rq -G https://qlever.cs.uni-freiburg.de/api/wikidata -o datasources/wikidata/recentData/gene.tsv + curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/geneHumanAllRedirects.rq -G https://qlever.dev/api/wikidata -o datasources/wikidata/recentData/gene.tsv ## Download outdated IDs for proteins qLever Style - curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/proteinHumanAllRedirects.rq -G https://qlever.cs.uni-freiburg.de/api/wikidata -o datasources/wikidata/recentData/protein.tsv + curl -H "Accept: text/tab-separated-values" --data-urlencode query@datasources/wikidata/queries/proteinHumanAllRedirects.rq -G https://qlever.dev/api/wikidata -o datasources/wikidata/recentData/protein.tsv ##Check new data, fail job if query timeout has occured @@ -89,6 +89,12 @@ jobs: head -n 20 "$File" #echo "DOWNLOAD_FILE=true" >>$GITHUB_ENV fail_file="${fail_file} $File" + elif grep -q "html" "$File"; then + echo "Data grab error occurred for file: " "$File" + echo "Wikidata data will not be updated" + head -n 20 "$File" + #echo "DOWNLOAD_FILE=true" >>$GITHUB_ENV + fail_file="${fail_file} $File" else echo "No Query Timeout detected for file: " "$File" fi diff --git a/datasources/wikidata/queries/chemicalAllRedirects.rq b/datasources/wikidata/queries/chemicalAllRedirects.rq index 8c4f5369..ab17dd20 100644 --- a/datasources/wikidata/queries/chemicalAllRedirects.rq +++ b/datasources/wikidata/queries/chemicalAllRedirects.rq @@ -10,12 +10,24 @@ WHERE { { ?primaryID p:P31/ps:P31 wd:Q11173 } UNION +{ ?primaryID wdt:P31 wd:Q11173 } +UNION { ?primaryID p:P31/ps:P31 wd:Q36496 } UNION +{ ?primaryID wdt:P31 wd:Q36496 } +UNION { ?primaryID p:P31/ps:P31 wd:Q79529 } UNION +{ ?primaryID wdt:P31 wd:Q79529 } +UNION { ?primaryID p:P31/ps:P31 wd:Q55662747 } UNION +{ ?primaryID wdt:P31 wd:Q55662747 } +UNION +{ ?primaryID p:P31/ps:31 wd:Q113145171 } +UNION +{ ?primaryID wdt:P31 wd:Q113145171 } +UNION { ?primaryID p:P279/ps:P279 wd:Q11173 } UNION { ?primaryID p:P279/ps:P279 wd:Q36496 } @@ -23,6 +35,9 @@ UNION { ?primaryID p:P279/ps:P279 wd:Q79529 } UNION { ?primaryID p:P279/ps:P279 wd:Q55662747 } +UNION +{ ?primaryID p:P279/ps:P279 wd:Q113145171 } + OPTIONAL{?secondaryID owl:sameAs ?primaryID.} OPTIONAL{?primaryID rdfs:label ?name. diff --git a/datasources/wikidata/queries/geneHumanAllRedirects.rq b/datasources/wikidata/queries/geneHumanAllRedirects.rq index 2ec9c0b3..95802287 100644 --- a/datasources/wikidata/queries/geneHumanAllRedirects.rq +++ b/datasources/wikidata/queries/geneHumanAllRedirects.rq @@ -10,6 +10,8 @@ WHERE { { ?primaryID p:P31/ps:P31 wd:Q7187 } UNION +{ ?primaryID wdt:P31 wd:Q7187 } +UNION { ?primaryID p:P279/ps:P279 wd:Q7187 } ?primaryID wdt:P703 wd:Q15978631. diff --git a/datasources/wikidata/queries/proteinHumanAllRedirects.rq b/datasources/wikidata/queries/proteinHumanAllRedirects.rq index 51f2508b..600442e4 100644 --- a/datasources/wikidata/queries/proteinHumanAllRedirects.rq +++ b/datasources/wikidata/queries/proteinHumanAllRedirects.rq @@ -10,6 +10,8 @@ WHERE { { ?primaryID p:P31/ps:P31 wd:Q8054 } UNION +{ ?primaryID wdt:P31 wd:Q8054 } +UNION { ?primaryID p:P279/ps:P279 wd:Q8054 } ?primaryID wdt:P703 wd:Q15978631.