from_uniprot is now easier to work with

weso · Jun 27, 2023 · aa74086 · aa74086
1 parent 6ab39bf
commit aa74086
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Showing 4 changed files with 16 additions and 1 deletion.
diff --git a/.gitignore b/.gitignore
@@ -14,4 +14,5 @@ Cargo.lock
 *.json
 *.duckdb
 *.nt
+*.rdf
 *.parquet
diff --git a/examples/from_uniprot/README.md b/examples/from_uniprot/README.md
@@ -0,0 +1,11 @@
+## Usage
+
+```{shell}
+cd examples/from_uniprot/
+sh run.sh
+```
+
+## Requirements
+
+Have the `xz` tool installed, as well as [Apache Jena's](https://jena.apache.org/documentation/tools/) `riot` command line utility
+installed.
diff --git a/examples/from_uniprot/main.rs b/examples/from_uniprot/main.rs
@@ -48,7 +48,7 @@ fn main() -> Result<(), String> {
     .into();
 
     // Load Wikidata entities
-    let edges = NTriples::import("./examples/from_uniprot/uniprotkb_reviewed_viruses_10239.nt")?;
+    let edges = NTriples::import("uniprotkb_reviewed_viruses_10239_0.nt")?;
 
     // Perform schema validation
     let start = Instant::now();

diff --git a/examples/from_uniprot/run.sh b/examples/from_uniprot/run.sh
@@ -0,0 +1,3 @@
+xz -v -d -k uniprotkb_reviewed_viruses_10239_0.rdf.xz
+riot --output=ntriples uniprotkb_reviewed_viruses_10239_0.rdf > uniprotkb_reviewed_viruses_10239_0.nt
+cargo run -r --example from_uniprot