SPARQLthon61/MicrobeDB.jp-Umakaviewer

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2017年10月24日 (火) 02:47時点におけるTfuji (トーク | 投稿記録)による版
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MicorbeDB.jpのSPARQL epに対して実行時の情報共有およびフィードバック

目次

metadataコマンドのヘルプ

%java -jar ../metadata-0.0.1-SNAPSHOT-jar-with-dependencies.jar
  Version: 20161212-1
Usage: java org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl [options]
   [options]
       1. to print a list of graphURIs
            -g endpointURL
       2. to crawl whole data in the endpoint
            -ac endpointURL crawlName outputFileName
       3. to crawl the specified graph in the endpoint
            -gc endpointURL crawlName graphURI outputFileName

フィードバック

versionが違う

→ バグフィックスの更新のため問題ない、山口さんに確認済み

crawlNameがどこで使われているか不明

outputFileNameはディレクトリの指定、ディレクトリがないと実行後にエラーになる

%java -jar ../metadata-0.0.1-SNAPSHOT-jar-with-dependencies.jar -ac http://localhost:18895/sparql mdb mdb_output.txt
log4j:WARN No appenders could be found for logger (org.apache.jena.riot.stream.JenaIOEnvironment).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
-----------------------------------------------------------
  Graph: http://microbedb.jp/assembly        1 / 33
-----------------------------------------------------------
/Users/tf/github/metadata/mdb_20171023/mdb_output.txt/turtle_mdb_assembly_1.ttl
P
properties
http://ddbj.nig.ac.jp/ontologies/nucleotide/dblink
http://www.ncbi.nlm.nih.gov/assembly/refseq_category
http://www.ncbi.nlm.nih.gov/assembly/asm_name
http://www.ncbi.nlm.nih.gov/assembly/assembly_level
http://www.ncbi.nlm.nih.gov/assembly/taxon
.
.
.
java.io.FileNotFoundException: /Users/tf/github/metadata/mdb_20171023/mdb_output.txt/turtle_mdb_assembly_1.ttl (No such file or directory)
    at java.io.FileOutputStream.open0(Native Method)
    at java.io.FileOutputStream.open(FileOutputStream.java:270)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
    at java.io.FileOutputStream.<init>(FileOutputStream.java:162)
    at org.sparqlbuilder.metadata.crawler.datastructure.SchemaCategory.write2File(SchemaCategory.java:20)
    at org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl.crawl(RDFsCrawlerImpl.java:270)
    at org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl.main(RDFsCrawlerImpl.java:86)
80747 msec.
Error occured.
Exception in thread "main" java.lang.Exception: Error occured s(341)
    at org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl.crawl(RDFsCrawlerImpl.java:286)
    at org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl.main(RDFsCrawlerImpl.java:86)
  • グラフ単位でも
%java -jar ../metadata-0.0.1-SNAPSHOT-jar-with-dependencies.jar -gc http://localhost:18893/sparql graph_18893 http://microbedb.jp/chebi chebi
  Version: 20161212-1
log4j:WARN No appenders could be found for logger (org.apache.jena.riot.stream.JenaIOEnvironment).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
-----------------------------------------------------------
  Graph: http://microbedb.jp/chebi        1 / 1
-----------------------------------------------------------
/Users/tf/github/metadata/mdb_20171023/chebi/turtle_graph_18893_chebi_1.ttl
.
.
.
#EndpointAccess: 161
java.io.FileNotFoundException: /Users/tf/github/metadata/mdb_20171023/chebi/turtle_graph_18893_chebi_1.ttl (No such file or directory)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(FileOutputStream.java:270)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:162)
	at org.sparqlbuilder.metadata.crawler.datastructure.SchemaCategory.write2File(SchemaCategory.java:20)
	at org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl.crawl(RDFsCrawlerImpl.java:270)
	at org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl.main(RDFsCrawlerImpl.java:103)
130204 msec.
Error occured.
Exception in thread "main" java.lang.Exception: Error occured s(341)
	at org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl.crawl(RDFsCrawlerImpl.java:286)
	at org.sparqlbuilder.metadata.crawler.sparql.RDFsCrawlerImpl.main(RDFsCrawlerImpl.java:103)

SPARQL ep.全体にかけたときは、fmaなど大きいオントロジーも入っていると終わらない

→ fma, taxonomy, so, sioなどを除きグラフ単位で取得に変更

%java -jar ../metadata-0.0.1-SNAPSHOT-jar-with-dependencies.jar -g http://localhost:18895/sparql
  Version: 20161212-1
log4j:WARN No appenders could be found for logger (org.apache.jena.riot.stream.JenaIOEnvironment).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.


不明なエラー出力された

ERROR: duplicate PDRD found! (L1144): 
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